Are you telling FSO to stop running when that warning appears? Because if so, that's the reason the subsystems aren't being written to the log file, because they get written after that Warning. Just hit "no" to continue when the warning pops up and then you should have your list of subsystems in the debug log.
EDIT: Whoops, let's not double-post:
Try this table entry (and the original, unmodified POF):
#ship classes
;-----------------------------------------------------------------
; Carrier Liberty
;-----------------------------------------------------------------
$Name: TCCV Liberty
$Short name: TLib
$Species: Terran
+Type: XSTR("Carrier", -1)
+Maneuverability: XSTR("Decent", -1)
+Armor: XSTR("Light", -1)
+Manufacturer: XSTR("", -1)
+Description: XSTR("", -1)
$end_multi_text
+Tech Description: XSTR("", -1)
$end_multi_text
+Length: XSTR("", -1)
+Gun Mounts: XSTR("16 turrets", -1)
$POF file: TCCV-Liberty.pof
$Detail distance: (0, 500, 1200, 5500)
$Show damage: YES
$Density: 1
$Damp: 0.1
$Rotdamp: 0.35
$Max Velocity: 0.0, 0.0, 30
$Rotation time: 65, 65, 65
$Rear Velocity: 0.0
$Forward accel: 4.5
$Forward decel: 1.3
$Slide accel: 0.0
$Slide decel: 0.0
$Expl inner rad: 150.0
$Expl outer rad: 750.0
$Expl damage: 200.0
$Expl blast: 11000.0
$Expl Propagates: YES
$Shockwave Speed: 400.0
$Shockwave Count: 3
$Default PBanks: ()
$Default SBanks: ()
$SBank Capacity: ()
$Shields: 20000
$Shield Color: 100 100 255
$Power Output: 4.5
$Max Oclk Speed: 33
$Max Weapon Eng: 150
$Hitpoints: 80000
$Flags: ("big damage" "cruiser" "in tech database" "flash")
$AI Class: Captain
$Afterburner: NO
$Countermeasures: 0
$Scan time: 2000
$EngineSnd: 128
$Closeup_pos: 0.0, 0.0, -500
$Closeup_zoom: 0.3
$Shield_icon: shield_liberty
$Score: 8
$Subsystem: turret01, 2.25, 1.0
$Armor Type: Everything
$Default PBanks: ( "Terran Turret" )
$Flags: ("check hull" "fire on target" "reset when idle")
$Subsystem: turret02, 2.25, 1.0
$Armor Type: Everything
$Default PBanks: ( "Terran Turret" )
$Flags: ("check hull" "fire on target" "reset when idle")
$Subsystem: turret03, 1.125, 1.0
$Armor Type: Everything
$Default PBanks: ( "Terran Turret" )
$Flags: ("check hull" "fire on target" "reset when idle")
$animation: triggered
$type: initial
+relative_angle: 90, 0, 0
$Subsystem: turret04, 1.125, 1.0
$Armor Type: Everything
$Default PBanks: ( "Terran Turret" )
$Flags: ("check hull" "fire on target" "reset when idle")
$animation: triggered
$type: initial
+relative_angle: 90, 0, 0
$Subsystem: turret05, 1.125, 1.0
$Armor Type: Everything
$Default PBanks: ( "Terran Turret" )
$Flags: ("check hull" "fire on target" "reset when idle")
$animation: triggered
$type: initial
+relative_angle: 90, 0, 0
$Subsystem: turret06, 1.125, 1.0
$Armor Type: Everything
$Default PBanks: ( "Terran Turret" )
$Flags: ("check hull" "fire on target" "reset when idle")
$animation: triggered
$type: initial
+relative_angle: 90, 0, 0
$Subsystem: turret07, .9375, 1.0
$Armor Type: Everything
$Default PBanks: ( "Terran Turret" )
$Flags: ("check hull" "fire on target" "reset when idle")
$animation: triggered
$type: initial
+relative_angle: 90, 180, 0
$Subsystem: turret08, .9375, 1.0
$Armor Type: Everything
$Default PBanks: ( "Terran Turret" )
$Flags: ("check hull" "fire on target" "reset when idle")
$animation: triggered
$type: initial
+relative_angle: 90, 0, 0
$Subsystem: turret09, .9375, 1.0
$Armor Type: Everything
$Default PBanks: ( "Terran Turret" )
$Flags: ("check hull" "fire on target" "reset when idle")
$animation: triggered
$type: initial
+relative_angle: 90, 0, 0
$Subsystem: turret10, .625, 1.0
$Armor Type: Everything
$Default PBanks: ( "Terran Turret" )
$Flags: ("check hull" "fire on target" "reset when idle")
$animation: triggered
$type: initial
+relative_angle: 90, 0, 0
$Subsystem: turret11, .625, 1.0
$Armor Type: Everything
$Default PBanks: ( "Terran Turret" )
$Flags: ("check hull" "fire on target" "reset when idle")
$animation: triggered
$type: initial
+relative_angle: 90, 0, 0
$Subsystem: turret12, .625, 1.0
$Armor Type: Everything
$Default PBanks: ( "Terran Turret" )
$Flags: ("check hull" "fire on target" "reset when idle")
$animation: triggered
$type: initial
+relative_angle: 90, 0, 0
$Subsystem: turret13, .625, 1.0
$Armor Type: Everything
$Default PBanks: ( "Terran Turret" )
$Flags: ("check hull" "fire on target" "reset when idle")
$animation: triggered
$type: initial
+relative_angle: 90, 180, 0
$Subsystem: turret14, .625, 1.0
$Armor Type: Everything
$Default PBanks: ( "Terran Turret" )
$Flags: ("check hull" "fire on target" "reset when idle")
$animation: triggered
$type: initial
+relative_angle: 90, 180, 0
$Subsystem: turret15, .625, 1.0
$Armor Type: Everything
$Default PBanks: ( "Blaziken Autocannon" )
$Flags: ("check hull" "fire on target" "reset when idle")
$animation: triggered
$type: initial
+relative_angle: 90, 180, 0
$Subsystem: turret16, .625, 1.0
$Armor Type: Everything
$Default PBanks: ( "Blaziken Autocannon" )
$Flags: ("check hull" "fire on target" "reset when idle")
$animation: triggered
$type: initial
+relative_angle: 90, 180, 0
$Subsystem: fighterbay1, 0, 0
$Flags: ( "carry no damage" "untargetable")
$Subsystem: fighterbay2, 0, 0
$Flags: ( "carry no damage" "untargetable")
$Subsystem: dish, 1, 0
$Flags: ( "carry no damage" "untargetable")
$Subsystem: Radar_Post, 1, 0
$Flags: ( "carry no damage" "untargetable")
$Subsystem: weapons, 1, 0
$Subsystem: engine01, 10, 0.0
$Engine Wash: Default300
$Subsystem: engine02, 10, 0.0
$Engine Wash: Default300
$Subsystem: engine03, 10, 0.0
$Engine Wash: Default300
$Subsystem: engine04, 10, 0.0
$Engine Wash: Default300
$Subsystem: engine05, 10, 0.0
$Engine Wash: Default300
$Subsystem: engine06, 10, 0.0
$Engine Wash: Default300
$Subsystem: engine07, 10, 0.0
$Engine Wash: Default300
$Subsystem: engine08, 10, 0.0
$Engine Wash: Default300
$Subsystem: intake01, 10, 0
$Flags: ("untargetable")
$Subsystem: intake02, 10, 0
$Flags: ("untargetable")
$Subsystem: intake03, 10, 0
$Flags: ("untargetable")
$Subsystem: intake04, 10, 0
$Flags: ("untargetable")
$Subsystem: intake05, 10, 0
$Flags: ("untargetable")
$Subsystem: intake06, 10, 0
$Flags: ("untargetable")
$Subsystem: intake07, 10, 0
$Flags: ("untargetable")
$Subsystem: intake08, 10, 0
$Flags: ("untargetable")
#end
The only warnings I get are two warnings that "Blaziken Autocannon" couldn't be found (which I presume you won't have).
