I'm running into a problem using this script.  I have used it successfully for implementing checkpoints twice before, but now I'm using it on a really complex checkpoint and it seems to be choking.  It saves all the ships, but it forgets all but one of the variables.
Here is the sexp that calls the scripts:
$Formula: ( when 
   ( and 
      ( is-event-true-delay 
         "mark clusters" 
         0 
      )
      ( is-event-true-delay 
         "Zeta Target Miners" 
         0 
      )
      ( is-event-true-delay 
         "Zeta Target SAC 3" 
         0 
      )
      ( is-event-true-delay 
         "phase 2 time limit" 
         0 
      )
      ( not 
         ( is-event-true-delay 
            "unsuccessful phase 2" 
            0 
         )
      )
   )
   ( modify-variable 
      "@filename[unset]" 
      "sa_m1_03_checkpoint1" 
   )
   ( script-eval "saveship('Alpha 1')" ) 
   ( script-eval "saveship('Beta 1')" ) 
   ( script-eval "saveship('Gamma 1')" ) 
   ( script-eval "saveship('Delta 1')" ) 
   ( script-eval "saveship('Zeta 1')" ) 
   ( script-eval "svar('random-seed')" ) 
   ( script-eval "svar('proximity_state')" ) 
   ( script-eval 
      "svar('AkihamCargoScanned')" 
   )
   ( script-eval 
      "svar('FighterProxBitfield')" 
   )
   ( script-eval-block 
      "svar('" 
      "ShipRecordBitfield_0_31')" 
   )
   ( script-eval-block 
      "svar('" 
      "ShipRecordBitfield_32_63')" 
   )
   ( script-eval-block 
      "svar('" 
      "ShipRecordBitfield_64_95')" 
   )
   ( script-eval-block 
      "svar('" 
      "ShipRecordBitfield_96_127')" 
   )
   ( script-eval 
      "svar('StealthStateInAsteroids')" 
   )
   ( script-eval "svar('StealthFlank')" ) 
   ( script-eval "svar('StealthFront')" ) 
   ( script-eval "svar('StealthScene')" ) 
   ( script-eval "svar('TargetACGLV')" ) 
   ( script-eval "svar('TargetAS')" ) 
   ( script-eval 
      "svar('TargetBhavisal')" 
   )
   ( script-eval "svar('TargetCP')" ) 
   ( script-eval "svar('TargetErebos')" ) 
   ( script-eval 
      "svar('TargetFreighters')" 
   )
   ( script-eval "svar('TargetMiners')" ) 
   ( script-eval "svar('TargetPCargo')" ) 
   ( script-eval "svar('TargetSCargo')" ) 
   ( script-eval "svar('TargetTotal')" ) 
   ( modify-variable 
      @sa_m1_03_checkpoint1[0] 
      1 
   )
   ( show-subtitle-text 
      "Checkpoint Reached!" 
      0 
      20 
      ( true ) 
      ( false ) 
      2000 
      2000 
   )
   ( script-eval "saveship('Akiham',3)" ) 
   ( script-eval "svar('AkihamState')" ) 
   ( script-eval 
      "saveship('Tauros 1',3)" 
   )
   ( script-eval "svar('Tauros1State')" ) 
   ( script-eval 
      "saveship('Tauros 2',3)" 
   )
   ( script-eval "svar('Tauros2State')" ) 
   ( script-eval 
      "saveship('Tauros 3',3)" 
   )
   ( script-eval "svar('Tauros3State')" ) 
   ( script-eval 
      "saveship('Tauros 4',3)" 
   )
   ( script-eval "svar('Tauros4State')" ) 
   ( script-eval 
      "saveship('Marduk 1',3)" 
   )
   ( script-eval "svar('Marduk1State')" ) 
   ( script-eval 
      "saveship('Marduk 2',3)" 
   )
   ( script-eval "svar('Marduk2State')" ) 
   ( script-eval 
      "saveship('Marduk 3',3)" 
   )
   ( script-eval "svar('Marduk3State')" ) 
   ( script-eval 
      "saveship('Marduk 4',3)" 
   )
   ( script-eval "svar('Marduk4State')" ) 
   ( script-eval 
      "saveship('Auroch 1',3)" 
   )
   ( script-eval "svar('Auroch1State')" ) 
   ( script-eval 
      "saveship('Auroch 2',3)" 
   )
   ( script-eval "svar('Auroch2State')" ) 
   ( script-eval 
      "saveship('Auroch 3',3)" 
   )
   ( script-eval "svar('Auroch3State')" ) 
   ( script-eval 
      "saveship('Auroch 4',3)" 
   )
   ( script-eval "svar('Auroch4State')" ) 
   ( script-eval "saveship('Nandi 1',3)" ) 
   ( script-eval "saveship('Nandi 2',3)" ) 
   ( script-eval "saveship('Nandi 3',3)" ) 
   ( script-eval "saveship('Nandi 4',3)" ) 
   ( script-eval 
      "saveship('Gugalana 1',3)" 
   )
   ( script-eval 
      "saveship('Gugalana 2',3)" 
   )
   ( script-eval 
      "saveship('Gugalana 3',3)" 
   )
   ( script-eval 
      "saveship('Gugalana 4',3)" 
   )
)
+Name: end of phase 2
+Repeat Count: 1
+Interval: 1
But here is the resulting save file.  Note that it has forgotten all but the Auroch4State variable.
§§§§§§§§§Auroch4State,n,1
Alpha 1,Beta 1,Gamma 1,Delta 1,Zeta 1,Akiham,Tauros 1,Tauros 2,Tauros 3,Tauros 4,Marduk 1,Marduk 2,Marduk 3,Marduk 4,Auroch 1,Auroch 2,Auroch 3,Auroch 4,Nandi 1,Nandi 2,Nandi 3,Nandi 4,Gugalana 1,Gugalana 2,Gugalana 3,Gugalana 4
1,GVF Ptah,Friendly,220,220,40,300,150,330,82.5,82.5,82.5,82.5,:5&22§-1,-1,-2&22§-1,-1,-2&22§-1,-1,-2&22§-1,-1,-2&77§-1,-1,-2&:1,0,0,Mekhu HL-7,1,0,-1,2,0,1,Harpoon,1,8,8,Hornet,0,10,10,-1:1749.4664306641,1945.6525878906,-6681.3193359375,0.2119675129652,0.84559243917465,0.4899420440197,-0.9258154630661,0.33428671956062,-0.17640353739262,-0.3129466176033,-0.41620409488678,0.85372048616409,-26.920928955078,-31.220394134521,80.040863037109,0.028319850564003,-0.20697958767414,0.10348979383707
-1,:::
-1,:::
-1,:::
-1,:::
1,SFr Asmodeus,Hostile,8000,8000,0,-1,-1,0,0,0,0,0,:9&160§1,0,0,Shivan Light Laser,0,0,-1,-1,-2&160§1,0,0,Standard Flak,0,0,-1,-1,-2&160§1,0,0,Shivan Light Laser,0,0,-1,-1,-2&160§1,0,0,Shivan Heavy Laser,0,0,-1,-1,-2&800§-1,-1,-2&800§-1,-1,-2&2800§-1,-1,-2&1200§-1,-1,-2&400§-1,-1,-2&:-1,-1,-1:2015.7319335938,2416.9699707031,-6971.810546875,0.76672065258026,0.0030975113622844,0.64197355508804,-3.1947376555763e-05,0.99998861551285,-0.0047867726534605,-0.64198106527328,0.0036496073007584,0.76671189069748,-9.9432001113892,0.056258119642735,12.779983520508,-7.8788480095682e-06,-0.052359879016876,-1.0372954420745e-05
1,SG Rahu,Hostile,15000,15000,0,-1,100,0,0,0,0,0,:9&8250§-1,-1,-2&750§1,0,0,Shivan Heavy Laser,0,0,-1,-1,-2&750§1,0,0,Shivan Heavy Laser,0,0,-1,-1,-2&750§1,0,0,Shivan Heavy Laser,0,0,-1,-1,-2&750§-1,-1,-2&300§-1,-1,-2&750§-1,-1,-2&750§-1,-1,-2&300§-1,-1,-2&:-1,-1,-1:-387.93002319336,2683.7058105469,141.72229003906,0.022241676226258,0.99865698814392,0.046793092042208,0.92409145832062,-0.0026743800844997,-0.38216230273247,-0.38152387738228,0.051741026341915,-0.92290979623795,-9.7253007888794,1.5225415229797,-22.98059463501,-0.0098177222535014,-0.013089870102704,-5.3543990361504e-06
1,SG Rahu,Hostile,15000,15000,0,-1,100,0,0,0,0,0,:9&8250§-1,-1,-2&750§1,0,0,Shivan Heavy Laser,0,0,-1,-1,-2&750§1,0,0,Shivan Heavy Laser,0,0,-1,-1,-2&750§1,0,0,Shivan Heavy Laser,0,0,-1,-1,-2&750§-1,-1,-2&300§-1,-1,-2&750§-1,-1,-2&750§-1,-1,-2&300§-1,-1,-2&:-1,-1,-1:-371.04776000977,1029.3172607422,1891.2720947266,-0.74798130989075,0.01705326884985,-0.66350078582764,-0.14498016238213,0.97133135795593,0.1884049475193,0.6476919054985,0.23711779713631,-0.7240651845932,2.0399961471558,17.785364151001,-1.8436107635498,0,0,0
1,SG Rahu,Hostile,15000,15000,0,-1,100,0,0,0,0,0,:9&8250§-1,-1,-2&750§1,0,0,Shivan Heavy Laser,0,0,-1,-1,-2&750§1,0,0,Shivan Heavy Laser,0,0,-1,-1,-2&750§1,0,0,Shivan Heavy Laser,0,0,-1,-1,-2&750§-1,-1,-2&300§-1,-1,-2&750§-1,-1,-2&750§-1,-1,-2&300§-1,-1,-2&:-1,-1,-1:-697.95867919922,1355.4770507813,3.6695795059204,0.99060279130936,-0.055693596601486,0.12491779029369,0.056748703122139,0.99837654829025,-0.0049011660739779,-0.12444201111794,0.011944029480219,0.9921550154686,0,0,0,-2.8025969286496e-45,2.8025969286496e-45,2.8025969286496e-45
1,SG Rahu,Hostile,15000,15000,0,-1,100,0,0,0,0,0,:9&8250§-1,-1,-2&750§1,0,0,Shivan Heavy Laser,0,0,-1,-1,-2&750§1,0,0,Shivan Heavy Laser,0,0,-1,-1,-2&750§1,0,0,Shivan Heavy Laser,0,0,-1,-1,-2&750§-1,-1,-2&300§-1,-1,-2&750§-1,-1,-2&750§-1,-1,-2&300§-1,-1,-2&:-1,-1,-1:414.72634887695,556.40447998047,-84.58536529541,0.98482799530029,0.020200338214636,-0.17235386371613,0.011632325127721,0.98328328132629,0.18171043694019,0.17314326763153,-0.18095837533474,0.96812987327576,0,0,0,-2.8025969286496e-45,2.8025969286496e-45,2.8025969286496e-45
1,SG Rahu,Hostile,15000,15000,0,-1,100,0,0,0,0,0,:9&8250§-1,-1,-2&750§1,0,0,Shivan Heavy Laser,0,0,-1,-1,-2&750§1,0,0,Shivan Heavy Laser,0,0,-1,-1,-2&750§1,0,0,Shivan Heavy Laser,0,0,-1,-1,-2&750§-1,-1,-2&300§-1,-1,-2&750§-1,-1,-2&750§-1,-1,-2&300§-1,-1,-2&:-1,-1,-1:-252.92047119141,1966.3835449219,1017.5070800781,-0.50716537237167,0.81865471601486,0.26942130923271,0.81662517786026,0.35653561353683,0.45387834310532,0.27551129460335,0.45020759105682,-0.84935653209686,2.225492477417,3.4630470275879,-6.3334193229675,0.039269909262657,8.3833304742598e-09,4.8773788563494e-08
1,SG Rahu,Hostile,15000,15000,0,-1,100,0,0,0,0,0,:9&8250§-1,-1,-2&750§1,0,0,Shivan Heavy Laser,0,0,-1,-1,-2&750§1,0,0,Shivan Heavy Laser,0,0,-1,-1,-2&750§1,0,0,Shivan Heavy Laser,0,0,-1,-1,-2&750§-1,-1,-2&300§-1,-1,-2&750§-1,-1,-2&750§-1,-1,-2&300§-1,-1,-2&:-1,-1,-1:1389.0887451172,985.52075195313,1873.6368408203,-0.68945723772049,-0.024940863251686,0.7238963842392,0.1892569065094,0.9584869146347,0.21327394247055,-0.69916516542435,0.28404608368874,-0.65611606836319,0,0,0,0,0,0
1,SG Rahu,Hostile,15000,15000,0,-1,100,0,0,0,0,0,:9&8250§-1,-1,-2&750§1,0,0,Shivan Heavy Laser,0,0,-1,-1,-2&750§1,0,0,Shivan Heavy Laser,0,0,-1,-1,-2&750§1,0,0,Shivan Heavy Laser,0,0,-1,-1,-2&750§-1,-1,-2&300§-1,-1,-2&750§-1,-1,-2&750§-1,-1,-2&300§-1,-1,-2&:-1,-1,-1:497.95657348633,980.94219970703,-236.01528930664,0.99938416481018,0.03196494281292,0.014573499560356,-0.026034750044346,0.95242595672607,-0.30365744233131,-0.023587238043547,0.30309188365936,0.95267045497894,0,0,0,0,0,0
1,SG Rahu,Hostile,15000,15000,0,-1,100,0,0,0,0,0,:9&8250§-1,-1,-2&750§1,0,0,Shivan Heavy Laser,0,0,-1,-1,-2&750§1,0,0,Shivan Heavy Laser,0,0,-1,-1,-2&750§1,0,0,Shivan Heavy Laser,0,0,-1,-1,-2&750§-1,-1,-2&300§-1,-1,-2&750§-1,-1,-2&750§-1,-1,-2&300§-1,-1,-2&:-1,-1,-1:502.50012207031,444.89120483398,1783.6767578125,-0.99976217746735,-0.0013449247926474,0.021768424659967,0.016912292689085,0.58241301774979,0.81271719932556,-0.013771256431937,0.81289196014404,-0.58225172758102,-0.079322904348373,-9.1715831756592,-8.3134927749634,-0.02126107364893,-0,-0
1,SG Rahu,Hostile,15000,15000,0,-1,100,0,0,0,0,0,:9&8250§-1,-1,-2&750§1,0,0,Shivan Heavy Laser,0,0,-1,-1,-2&750§1,0,0,Shivan Heavy Laser,0,0,-1,-1,-2&750§1,0,0,Shivan Heavy Laser,0,0,-1,-1,-2&750§-1,-1,-2&300§-1,-1,-2&750§-1,-1,-2&750§-1,-1,-2&300§-1,-1,-2&:-1,-1,-1:1560.4761962891,1216.4621582031,-134.83256530762,-0.44461166858673,0.033565573394299,0.89509433507919,0.079608127474785,0.99682402610779,0.0021626011002809,-0.89217889308929,0.072218306362629,-0.44587162137032,-12.260375022888,0.99243462085724,-6.1271953582764,0,0,0
1,SG Rahu,Hostile,15000,15000,0,-1,100,0,0,0,0,0,:9&8250§-1,-1,-2&750§1,0,0,Shivan Heavy Laser,0,0,-1,-1,-2&750§1,0,0,Shivan Heavy Laser,0,0,-1,-1,-2&750§1,0,0,Shivan Heavy Laser,0,0,-1,-1,-2&750§-1,-1,-2&300§-1,-1,-2&750§-1,-1,-2&750§-1,-1,-2&300§-1,-1,-2&:-1,-1,-1:1967.5775146484,1490.1624755859,967.74774169922,-0.015821624547243,0.0021374630741775,0.99987250566483,0.011283962056041,0.9999343752861,-0.0019590419251472,-0.99981111288071,0.011251525953412,-0.015844708308578,-16.519058227539,0.56184715032578,-0.63938641548157,0.039267908781767,0.039271909743547,-2.2700987756252e-09
1,SG Rahu,Hostile,15000,15000,0,-1,100,0,0,0,0,0,:9&8250§-1,-1,-2&750§1,0,0,Shivan Heavy Laser,0,0,-1,-1,-2&750§1,0,0,Shivan Heavy Laser,0,0,-1,-1,-2&750§1,0,0,Shivan Heavy Laser,0,0,-1,-1,-2&750§-1,-1,-2&300§-1,-1,-2&750§-1,-1,-2&750§-1,-1,-2&300§-1,-1,-2&:-1,-1,-1:2555.3361816406,1438.9107666016,905.05975341797,0.55889397859573,-0.18078395724297,0.80929273366928,0.63395726680756,0.72226411104202,-0.2764650285244,-0.53454262018204,0.66757160425186,0.51827836036682,-13.367321014404,16.685007095337,12.958599090576,0.00056615460198373,-4.3055409980897e-16,-6.3940339134483e-11
1,SG Rahu,Hostile,15000,15000,0,-1,100,0,0,0,0,0,:9&8250§-1,-1,-2&750§1,0,0,Shivan Heavy Laser,0,0,-1,-1,-2&750§1,0,0,Shivan Heavy Laser,0,0,-1,-1,-2&750§1,0,0,Shivan Heavy Laser,0,0,-1,-1,-2&750§-1,-1,-2&300§-1,-1,-2&750§-1,-1,-2&750§-1,-1,-2&300§-1,-1,-2&:-1,-1,-1:2628.9907226563,914.78259277344,1227.3508300781,-0.38969203829765,-0.085560120642185,0.91696220636368,-0.35064280033112,0.9344664812088,-0.061823315918446,-0.85158079862595,-0.34561821818352,-0.39415517449379,-21.289522171021,-8.6404581069946,-9.8538846969604,0,0,0
1,SFr Dis,Hostile,7000,7000,0,-1,-1,0,0,0,0,0,:9&140§1,0,0,Shivan Light Laser,0,0,-1,-1,-2&140§1,0,0,Shivan Light Laser,0,0,-1,-1,-2&140§1,0,0,Standard Flak,0,0,-1,-1,-2&140§1,0,0,Standard Flak,0,0,-1,-1,-2&700§-1,-1,-2&700§-1,-1,-2&2450§-1,-1,-2&1050§-1,-1,-2&350§-1,-1,-2&:-1,-1,-1:-12692.14453125,1075.083984375,-9313.240234375,-0.00013404585479293,0.99796831607819,0.063713036477566,0.00105993647594,0.063713148236275,-0.99796783924103,-0.99999952316284,-6.62416787236e-05,-0.0010663233697414,-42.00297164917,-0.0027823492418975,-0.044788770377636,-0,-0,-0
1,SFr Dis,Hostile,7000,7000,0,-1,-1,0,0,0,0,0,:9&140§1,0,0,Shivan Light Laser,0,0,-1,-1,-2&140§1,0,0,Shivan Light Laser,0,0,-1,-1,-2&140§1,0,0,Standard Flak,0,0,-1,-1,-2&140§1,0,0,Standard Flak,0,0,-1,-1,-2&700§-1,-1,-2&700§-1,-1,-2&2450§-1,-1,-2&1050§-1,-1,-2&350§-1,-1,-2&:-1,-1,-1:-12335.026367188,1074.5417480469,-8114.462890625,-0.00015267438720912,0.9978329539299,0.065798848867416,0.0013103621313348,0.065798997879028,-0.99783211946487,-0.99999916553497,-6.6123095166404e-05,-0.0013175681233406,-42.00297164917,-0.0027773682959378,-0.055341817438602,-0,0,-0
1,SFr Dis,Hostile,7000,7000,0,-1,-1,0,0,0,0,0,:9&140§1,0,0,Shivan Light Laser,0,0,-1,-1,-2&140§1,0,0,Shivan Light Laser,0,0,-1,-1,-2&140§1,0,0,Standard Flak,0,0,-1,-1,-2&140§1,0,0,Standard Flak,0,0,-1,-1,-2&700§-1,-1,-2&700§-1,-1,-2&2450§-1,-1,-2&1050§-1,-1,-2&350§-1,-1,-2&:-1,-1,-1:-12071.549804688,1073.9110107422,-6917.3559570313,-0.00016516138566658,0.99799358844757,0.063314735889435,0.001561131211929,0.06331492215395,-0.99799239635468,-0.9999988079071,-6.5987194830086e-05,-0.0015684560639784,-42.002956390381,-0.0027716606855392,-0.065879851579666,0,0,-0
1,SFr Dis,Hostile,7000,7000,0,-1,-1,0,0,0,0,0,:9&140§1,0,0,Shivan Light Laser,0,0,-1,-1,-2&140§1,0,0,Shivan Light Laser,0,0,-1,-1,-2&140§1,0,0,Standard Flak,0,0,-1,-1,-2&140§1,0,0,Standard Flak,0,0,-1,-1,-2&700§-1,-1,-2&700§-1,-1,-2&2450§-1,-1,-2&1050§-1,-1,-2&350§-1,-1,-2&:-1,-1,-1:-11681.903320313,1078.8231201172,-6319.19921875,-0.00018842735153157,0.99741989374161,0.071788139641285,0.0016845333157107,0.071788363158703,-0.99741852283478,-0.99999862909317,-6.7011424107477e-05,-0.0016937139444053,-42.002952575684,-0.0028146819677204,-0.071141093969345,-0,0,-0
1,SFr Dis,Hostile,7000,7000,0,-1,-1,0,0,0,0,0,:9&140§1,0,0,Shivan Light Laser,0,0,-1,-1,-2&140§1,0,0,Shivan Light Laser,0,0,-1,-1,-2&140§1,0,0,Standard Flak,0,0,-1,-1,-2&140§1,0,0,Standard Flak,0,0,-1,-1,-2&700§-1,-1,-2&700§-1,-1,-2&2450§-1,-1,-2&1050§-1,-1,-2&350§-1,-1,-2&:-1,-1,-1:-2279.6684570313,1432.3571777344,-5967.4145507813,0.0037887820508331,0.00094227399677038,-0.99999243021011,-0.00079163914779201,0.99999934434891,0.00093928113346919,0.9999925494194,0.00078807427780703,0.003789525013417,42.00269317627,0.033102300018072,0.15917903184891,0,0,0
1,SFr Dis,Hostile,7000,7000,0,-1,-1,0,0,0,0,0,:9&140§1,0,0,Shivan Light Laser,0,0,-1,-1,-2&140§1,0,0,Shivan Light Laser,0,0,-1,-1,-2&140§1,0,0,Standard Flak,0,0,-1,-1,-2&140§1,0,0,Standard Flak,0,0,-1,-1,-2&700§-1,-1,-2&700§-1,-1,-2&2450§-1,-1,-2&1050§-1,-1,-2&350§-1,-1,-2&:-1,-1,-1:-2695.1577148438,1432.0119628906,-6573.1518554688,-0.0044539640657604,0.00052171957213432,-0.99998992681503,-0.00079270644346252,0.99999958276749,0.00052525533828884,0.99998980760574,0.00079503800952807,-0.0044535486958921,42.002578735352,0.033392697572708,-0.18706528842449,0,0,0
1,SFr Dis,Hostile,7000,7000,0,-1,-1,0,0,0,0,0,:9&140§1,0,0,Shivan Light Laser,0,0,-1,-1,-2&140§1,0,0,Shivan Light Laser,0,0,-1,-1,-2&140§1,0,0,Standard Flak,0,0,-1,-1,-2&140§1,0,0,Standard Flak,0,0,-1,-1,-2&700§-1,-1,-2&700§-1,-1,-2&2450§-1,-1,-2&1050§-1,-1,-2&350§-1,-1,-2&:-1,-1,-1:-3007.9592285156,1431.8013916016,-7171.7045898438,-0.012268927879632,0.0037197540514171,-0.99991780519485,-0.00073440955020487,0.99999284744263,0.0037290442269295,0.99992454051971,0.00078010058496147,-0.012266108766198,41.999839782715,0.032766491174698,-0.51521396636963,-0,-0,-0
1,SFr Dis,Hostile,7000,7000,0,-1,-1,0,0,0,0,0,:9&140§1,0,0,Shivan Light Laser,0,0,-1,-1,-2&140§1,0,0,Shivan Light Laser,0,0,-1,-1,-2&140§1,0,0,Standard Flak,0,0,-1,-1,-2&140§1,0,0,Standard Flak,0,0,-1,-1,-2&700§-1,-1,-2&700§-1,-1,-2&2450§-1,-1,-2&1050§-1,-1,-2&350§-1,-1,-2&:-1,-1,-1:-3320.037109375,1431.6094970703,-7765.5537109375,-0.020158337429166,0.0045972722582519,-0.99978625774384,-0.0006685794214718,0.9999892115593,0.0046116858720779,0.99979662895203,0.00076140038436279,-0.020155046135187,41.994464874268,0.031982272863388,-0.84656834602356,0,0,0
I looked in fs2_open.log and the script seems to know about the variables, at least.  (I wish the logging used newlines here, but at least I can follow what it's doing):
random-seed,n,698random-seed,n,698&proximity_state,n,1random-seed,n,698&proximity_state,n,1&AkihamCargoScanned,n,1random-seed,n,698&proximity_state,n,1&AkihamCargoScanned,n,1&FighterProxBitfield,n,12288random-seed,n,698&proximity_state,n,1&AkihamCargoScanned,n,1&FighterProxBitfield,n,12288&ShipRecordBitfield_0_31,n,-2129657859random-seed,n,698&proximity_state,n,1&AkihamCargoScanned,n,1&FighterProxBitfield,n,12288&ShipRecordBitfield_0_31,n,-2129657859&ShipRecordBitfield_32_63,n,2147438863random-seed,n,698&proximity_state,n,1&AkihamCargoScanned,n,1&FighterProxBitfield,n,12288&ShipRecordBitfield_0_31,n,-2129657859&ShipRecordBitfield_32_63,n,2147438863&ShipRecordBitfield_64_95,n,1010270175random-seed,n,698&proximity_state,n,1&AkihamCargoScanned,n,1&FighterProxBitfield,n,12288&ShipRecordBitfield_0_31,n,-2129657859&ShipRecordBitfield_32_63,n,2147438863&ShipRecordBitfield_64_95,n,1010270175&ShipRecordBitfield_96_127,n,968random-seed,n,698&proximity_state,n,1&AkihamCargoScanned,n,1&FighterProxBitfield,n,12288&ShipRecordBitfield_0_31,n,-2129657859&ShipRecordBitfield_32_63,n,2147438863&ShipRecordBitfield_64_95,n,1010270175&ShipRecordBitfield_96_127,n,968&StealthStateInAsteroids,n,0random-seed,n,698&proximity_state,n,1&AkihamCargoScanned,n,1&FighterProxBitfield,n,12288&ShipRecordBitfield_0_31,n,-2129657859&ShipRecordBitfield_32_63,n,2147438863&ShipRecordBitfield_64_95,n,1010270175&ShipRecordBitfield_96_127,n,968&StealthStateInAsteroids,n,0&StealthFlank,n,200random-seed,n,698&proximity_state,n,1&AkihamCargoScanned,n,1&FighterProxBitfield,n,12288&ShipRecordBitfield_0_31,n,-2129657859&ShipRecordBitfield_32_63,n,2147438863&ShipRecordBitfield_64_95,n,1010270175&ShipRecordBitfield_96_127,n,968&StealthStateInAsteroids,n,0&StealthFlank,n,200&StealthFront,n,300random-seed,n,698&proximity_state,n,1&AkihamCargoScanned,n,1&FighterProxBitfield,n,12288&ShipRecordBitfield_0_31,n,-2129657859&ShipRecordBitfield_32_63,n,2147438863&ShipRecordBitfield_64_95,n,1010270175&ShipRecordBitfield_96_127,n,968&StealthStateInAsteroids,n,0&StealthFlank,n,200&StealthFront,n,300&StealthScene,n,1random-seed,n,698&proximity_state,n,1&AkihamCargoScanned,n,1&FighterProxBitfield,n,12288&ShipRecordBitfield_0_31,n,-2129657859&ShipRecordBitfield_32_63,n,2147438863&ShipRecordBitfield_64_95,n,1010270175&ShipRecordBitfield_96_127,n,968&StealthStateInAsteroids,n,0&StealthFlank,n,200&StealthFront,n,300&StealthScene,n,1&TargetACGLV,n,9random-seed,n,698&proximity_state,n,1&AkihamCargoScanned,n,1&FighterProxBitfield,n,12288&ShipRecordBitfield_0_31,n,-2129657859&ShipRecordBitfield_32_63,n,2147438863&ShipRecordBitfield_64_95,n,1010270175&ShipRecordBitfield_96_127,n,968&StealthStateInAsteroids,n,0&StealthFlank,n,200&StealthFront,n,300&StealthScene,n,1&TargetACGLV,n,9&TargetAS,n,4random-seed,n,698&proximity_state,n,1&AkihamCargoScanned,n,1&FighterProxBitfield,n,12288&ShipRecordBitfield_0_31,n,-2129657859&ShipRecordBitfield_32_63,n,2147438863&ShipRecordBitfield_64_95,n,1010270175&ShipRecordBitfield_96_127,n,968&StealthStateInAsteroids,n,0&StealthFlank,n,200&StealthFront,n,300&StealthScene,n,1&TargetACGLV,n,9&TargetAS,n,4&TargetBhavisal,n,1random-seed,n,698&proximity_state,n,1&AkihamCargoScanned,n,1&FighterProxBitfield,n,12288&ShipRecordBitfield_0_31,n,-2129657859&ShipRecordBitfield_32_63,n,2147438863&ShipRecordBitfield_64_95,n,1010270175&ShipRecordBitfield_96_127,n,968&StealthStateInAsteroids,n,0&StealthFlank,n,200&StealthFront,n,300&StealthScene,n,1&TargetACGLV,n,9&TargetAS,n,4&TargetBhavisal,n,1&TargetCP,n,4random-seed,n,698&proximity_state,n,1&AkihamCargoScanned,n,1&FighterProxBitfield,n,12288&ShipRecordBitfield_0_31,n,-2129657859&ShipRecordBitfield_32_63,n,2147438863&ShipRecordBitfield_64_95,n,1010270175&ShipRecordBitfield_96_127,n,968&StealthStateInAsteroids,n,0&StealthFlank,n,200&StealthFront,n,300&StealthScene,n,1&TargetACGLV,n,9&TargetAS,n,4&TargetBhavisal,n,1&TargetCP,n,4&TargetErebos,n,0random-seed,n,698&proximity_state,n,1&AkihamCargoScanned,n,1&FighterProxBitfield,n,12288&ShipRecordBitfield_0_31,n,-2129657859&ShipRecordBitfield_32_63,n,2147438863&ShipRecordBitfield_64_95,n,1010270175&ShipRecordBitfield_96_127,n,968&StealthStateInAsteroids,n,0&StealthFlank,n,200&StealthFront,n,300&StealthScene,n,1&TargetACGLV,n,9&TargetAS,n,4&TargetBhavisal,n,1&TargetCP,n,4&TargetErebos,n,0&TargetFreighters,n,4random-seed,n,698&proximity_state,n,1&AkihamCargoScanned,n,1&FighterProxBitfield,n,12288&ShipRecordBitfield_0_31,n,-2129657859&ShipRecordBitfield_32_63,n,2147438863&ShipRecordBitfield_64_95,n,1010270175&ShipRecordBitfield_96_127,n,968&StealthStateInAsteroids,n,0&StealthFlank,n,200&StealthFront,n,300&StealthScene,n,1&TargetACGLV,n,9&TargetAS,n,4&TargetBhavisal,n,1&TargetCP,n,4&TargetErebos,n,0&TargetFreighters,n,4&TargetMiners,n,6random-seed,n,698&proximity_state,n,1&AkihamCargoScanned,n,1&FighterProxBitfield,n,12288&ShipRecordBitfield_0_31,n,-2129657859&ShipRecordBitfield_32_63,n,2147438863&ShipRecordBitfield_64_95,n,1010270175&ShipRecordBitfield_96_127,n,968&StealthStateInAsteroids,n,0&StealthFlank,n,200&StealthFront,n,300&StealthScene,n,1&TargetACGLV,n,9&TargetAS,n,4&TargetBhavisal,n,1&TargetCP,n,4&TargetErebos,n,0&TargetFreighters,n,4&TargetMiners,n,6&TargetPCargo,n,16random-seed,n,698&proximity_state,n,1&AkihamCargoScanned,n,1&FighterProxBitfield,n,12288&ShipRecordBitfield_0_31,n,-2129657859&ShipRecordBitfield_32_63,n,2147438863&ShipRecordBitfield_64_95,n,1010270175&ShipRecordBitfield_96_127,n,968&StealthStateInAsteroids,n,0&StealthFlank,n,200&StealthFront,n,300&StealthScene,n,1&TargetACGLV,n,9&TargetAS,n,4&TargetBhavisal,n,1&TargetCP,n,4&TargetErebos,n,0&TargetFreighters,n,4&TargetMiners,n,6&TargetPCargo,n,16&TargetSCargo,n,14Frame 5462 too long!!: frametime = 1.335 (1.335)
It looks like it's saving variables just fine up until it gets to TargetTotal.  Then, at least, it stops writing to the log.  It still saved Auroch4State despite this variable not appearing in the log.