Upgraded to Mountain Lion a few weeks ago, didn't have the problem. A few days ago I replaced the hard drive with a SSD and did a clean install of Mountain Lion then manually moved my background images to the new drive. I added the folders to the sidebar in the
System Preferences > Desktop & Screensaver panel. After closing it and reopening it, every folder but the last selected folder is gone.
I tried removing
~/Library/Preferences/com.apple.systempreferences.plist then rebooted and the problem remained.
Steps to reproduce:
- Open System Preferences > Desktop
- Add Folder A to panel
- Add Folder B to panel
- Open Folder B and choose image from it to set desktop
- Click Folder A to browse it
- Close System Preferences
- Reopen System Preferences > Desktop
- See that Folder A remains
Video screenshot: http://www.youtube.com/watch?v=1Qy01PS0aT0