I have to admit, the Mission end part is one of the more mysterious parts of BC. I know of your problem, mine happens occasionally when I want to stop a mission, in fact, if I press the Quit button BC just stops.
At the moment, I don't know of a solution for this. I suspect it's that not all scripts don't play nice (unintentionally, like I said, this part of BC is hardly explored).
About the save games, it doesn't create them at all?
How many are there?