How the hell are you supposed to kill a Shivan? The ML-16's can't scratch their fighters.
EDIT: Oh, yes, I just remembered. I'm having a persistent crash in mission 7, right after the cargo depot blows up, when that next wing of Shivan fighters jumps in. This is in 3.6.5's main build.
EDIT2: Oh, yes. I checked it using both Goober 12/15 build and Bob's 12/04 build, it still crashes. It doesn't seem keyed to the arrival of new fighters but rather to the New Orders #1 directive, but I'm not sure...
Third and final edit: Never mind, never mind. I found the problem after it crept up somewhere else. "Loads only used weapons" is poison on my system. Remove it, everything starts working.