Desktop & Screensaver won't store my changes

Sounds like it might be a bug, triggered when you move or delete a folder that is currently shown in the sidebar of that System Preferences pane.

What happens if you do this...? Put new folders back where those "ghost" folders were previously located. They don't have to have anything in them, but give them the same names as before. Then open System Preferences to the Desktop pane and try to remove the folders from the sidebar. Are they now gone permanently?

Sounds like you have corrupt prefs for Desktop and Screensaver. Go to your home folder /Library/Preferences/ and locate a file called com.apple.preference.desktopscreeneffect.plist and delete it. Also, get rid of the lock file associated with it. Log off and log back in. Then, launch System Preferences, and go back to Desktop and Screensaver.

I haven't tried this myself yet, but it's the first thing that I would do if I had this problem. You're not going to hurt anything. It should just reset the preferences for Desktop and Screensaver back to their defaults. You might see your desktop background change back to Lion's default Galaxy background.

On Finder's menubar, Finder > Go > hold option key down > select Library.

In the Preferences folder, delete com.apple.desktop.plist.

Logoff/Logon

I have the same problem and tried deleting the preference files detailed in this post. It's gotten rid of all my old wallpaper folders which is what I wanted but if I add new ones in it doesn't remember them and when I go into Desktop the new folders have disappeared. If I'm currently using a wallpaper in an added folder then it doesn't initially appear but after a second or two it will force itself to show up.

Zap your PRAM

Shut down and start up holding Command , Option, P, and R.

Wait for the chime to sound twice

Sorry, didn't work.

Make sure you are on Finder's menu> Go > hold option key down and select Library.

Look for Preferences folder and drag com.apple.finder.plist to Desktop. Reboot

That hasn't worked either I'm afraid.

Same problem (folders added to Desktop Preferences via the bottom + menu or drag n' drop don't save) on Mountain Lion. None of the above solutions worked, but thanks anyway for helping. BTW, I'm running 10.8.3 on a 15" rMBP.

Also, what does zapping the PRAM mean, and when would it be advisable?

I'm on 10.8.2 and am having the same problem. We need a new fix!

Hope this thread can fix the issue

https://discussions.apple.com/thread/4793021?start=0&tstart=0

Try booting on safe boot then try the folders or check settings then reboot again to normal.

http://support.apple.com/kb/ht1455

To start up into Safe Mode (to Safe Boot), do this:

1. Be sure your Mac is shut down.
2. Press the power button.
3. Immediately after you hear the startup tone, hold the Shift key. The Shift key should be held as soon as possible after the startup tone, but not before the tone.
4. Release the Shift key when you see the gray Apple icon and the progress indicator (looks like a spinning gear).

To reboot as normal just restart the Mac.

Second option

Try to delete Saved application state of your finder.

1. Finder Menu>GO (then hold Alt/option to reveal Library) Click on Library

2. Look for the Saved Application State Folder and delete com.apple.findersavedState. Reboot the machine so that it will create a new fresh findersavedstate file

Might set your finder to default again though. Hope it it helps.

@whaletail935, "zapping" the PRAM is referring to a process that resets certain hardware settings on your Mac.

See http://support.apple.com/kb/ph11243 for details.

However, the issue being discussed in this thread is a software issue, so doing anything to the PRAM will not likely have any affect on what we're trying to fix.

Secondly, I'm having the same issue as detailed here: https://discussions.apple.com/thread/4940397

Assistance with this would be excellent...