I used PSE 11 File-Import-from scanner. The scanner is a Canon 8400F.Then I use Save As... I am running OS 10.8.2.
If I use the Canon toolbox app to scan the image I get an image as scan2a in the finder.
If I just open scan2a in Graphics Converter then immediately Save as... I get scan2a. So somehow GC fixes the problem.
Try going to your username>library>preferences and deleting:
Adobe Photoshop Elements 11 paths
Adobe Photoshp Elements settings
That library is hidden in 10.8. To see it, option click the Go menu in the Finder. It will appear below the little house for your user account. While you're in there, delete anything pertaining to PSE from the Saved Application States folder.
Repair permissions and try again.
Never replace those files. They regenerate automatically on the next editor launch. Whatever your problem was it had nothing to do with deleting those, I'm afraid, so you'll probably see it again.
I am still interested in help on this subject. Additional Info: If I save as TIFF I get the same results. If I open the saved by PSE in Preview then do an export then the picture on the desktop is fine.