a) There is no such things as a deliberate order to scan the fighters in that mission ...
Then it must have been a bug caused by using 3.6.12INF without Zathras. I tried it several times and the dead Gorith 5 never triggered the mission update although it was scanned.
I continued with this otherwise excellent campaign and found some more issues that may be worth looking into:
In the mission in which one needs to defend the two Narn cruisers against a Centauri cruiser with Drakh fighters I never could keep the cruisers alive on very easy, even when I destroyed the Primus' laser turrets myself. I set the health of the damaged Narn cruiser to 100 in the mission file and still barely managed to do it. So either I'm really bad or this mission is too difficult with the new engine and patch features!
I'm now near the end of part 3 in which I only found some minor stuff. In the first mission the starting location and default speed of your fighter has it ending up in the docking bay if you don't at once fly away which looks strange
! Also in some of the mission descriptions and subtitles there are a lot of typos and spelling errors, much more than in the earlier mission texts. This is true BTW for a lot of campaigns.
On the whole though, my compliments on a great campaign pack
! I liked the story and especially the short non-fighting missions that kept it going on. I hope the ending is satisfying although looking at the way the Drakh cruisers are using their powerbeams with the Narn and EA cruisers ignoring their own, I fear the mission in which the station is destroyed maybe another candidate for engine and patch tweaking...