This was happening to me, too. David added some loading conditions to pick the newest save file, but they don't seem to help. I don't really think that's the problem -- I think the recent save file just reverts... maybe save and exit isn't writing to disk at all.
It's hard to predict, but to prevent it from happening I always make a backup after I save/exit by going into continue game from the main menu. This has added benefits for Iron Man games