Common Problem, they are looking into and as you have discovered, the workaround is to use manual saves. I believe they have disabled the Steam Cloud for this game, but keep doing what you are doing as it is better anyway.
They are looking into this matter and when the announcement is made we will let you all know.
I am going to close this as we have a discussion on this already.

http://www.gamesas.com/index.php?/topic/1122356-problems-with-save-games/