I have a similar probleme! Do you got an error code? If you find a way to recover those save, it me up!
Looks like someone else had this issue with their auto save here
http://forums.larian.com/ubbthreads.php?ubb=showflat&Number=679592&gonew=1#UNREADThey found the fix. In Steam, right click on this game and go to Properties>Updates, and uncheck the cloud saves option. That fixed it for me.
EDIT: Nevermind, it did not fix the issue of actually quick saving.