I believe this is completely related to the Steam Cloud Save issue, I will close this and see my post in this thread, #45
http://www.gamesas.com/index.php?/topic/1122356-problems-with-save-games/page__st__40
This explains how things are getting shuffled and your saves seem to be missing things. Try what I have suggested, and let me know. If it does not resolve it, then I will reopen this one.