Is the scramble mission you're talking about the little in-mission briefing, with the button to continue on the lower right? Sometimes those will crash me. The best solution I can think of is to just take off the Red Alert flag in FRED- it will allow you to choose your ship, but to be honest, I don't really know of any other way. IIRC, Homesick had a lot of those, so I don't know what to do, other than continually editing the mission file, to help.
I dont't know what causes the problem, but I heard that the bug will be fixed in 3.6.10.
You can also run a debug build to give us a more precise error message.