Do you use Windows 7? I'm holding off on the patch, but it may have made it so windows is putting the saves in the virtual store.
check to see if there's a stardock (and e:wom sub-directories) in your C:\Users\*yourusername*\AppData\Local\VirtualStore\Program Files (x86) directory. if a permissions setting was changed (ie something lost admin privelege or a directory was changed so that your current user lost ownership) then that is where windows likes to put changes made to any "programfiles" folders in terms of new files.
Took me forever to realize that's where my fallout 2 and baldur's gate savegames were hiding. I also think that files placed there do not show up in a normal search either since those virtual store folders are non-indexed by default.
