I did use the pilot for multiple mods, which is why I never really tried to get the issue solved. I assumed it was unique to me because I was stupid enough not to use separate pilots. And no, I think I was running RC2 at the time. Another oddity is that there is no fail mission debrief for that level.
Mind you, I did have a "wtf" moment when my wingman said "WE'RE ALL DOOMED" and the mission failed on me. I thought to myself that that couldn't possibly have been the end of the campaign, and I was relieved that I was right.
Meh. I'm on a new machine now, and if I ever feel like replaying BP, I know what to do