@maxjoiner:
Two things need clarifying:
1. You say you save a mission, do you mean you save a mission while playing (press ESC - Save Game) it or do you mean you save a mission in the editor?
2. You say the scripts don't work, how exactly? Error messages?
EDIT:
Hmm, if the script is a short non-looping script, it has already been executed via a trigger and run through, and then the game is saved the trigger will not be run again after the savegame reload because it already has done it's job.
Also, there has been in the past savegame incompatability with a few of the scripting commands, at least setObjectTexture and animate "don't work" in OFP (CWA) and A1; as in their states don't get saved in a savegame (dunno what's the situation with A2). IIRC the same problem was with the command switchLight.