I was playing with my FRED and Freespace (All-retail versions, in case your interested) making up random battles with the Inferno ships.
At one moment, i had Alpha luanching from the Nemesis. I origionally had a Claymore MK2, and set it to the docking bay of the Nemesis. But then i changed to the GTF Alves, and when i pressed commit on the breifing screen, the game crashed to desktop with no debug information.
I then changed back to an EF ship, and it worked fine.
I don't know anything about programming this deep, but it seems that some of the fighters arn't compatible with the fighterbays of certain capital ships. I thought maybe some of the team could look into it if they have some spare time.
T-Man