Well, this time when I approached the Ctoth, I didn't use my afterburners and I didn't put all my energy into the engines. Then it didn't randomly exit.
Want to hear another wierd thing? I was just replaying the main FS2 campaign and I got to the mission where you go undercover as a rebel (the first one in that loop). It says to go scan the Iceni. I target the Iceni and guess what it turned out to be? A Ulysses class fighter.
EDIT: And guess what fixed that Iceni being a fighter thing. Deleting the Derelict campaign VP file fixed it. Derelict was good though, I really did enjoy it.