Just to clarify the facts:
- This behaviour occurs when calling "gksu nautilus" in Ubuntu 12.04 with 
latest updates installed
- Until now, I did not managed to manually remove the root wallpaper after it 
was loaded
- The dialog for changing the wallpaper is run in root context after 
reproducing the situation when called via right click on the desktop
- Several (additional, gui related) root processes stays in background even 
after closing nautilus a long time ago
- Killing some of them prevents right clicks on the desktop, so the dialog for 
changing the wallpaper with root rights is not accessible anymore
- Also files/starter from the root desktop folder are shown on the desktop
- This also works with another account than root

I could not reproduce it on all machines though!
Machine 1 (affected): fresh install of 12.04
Machine 2 (affected): 12.04 upgraded from several prior versions
Machine 3 (not affected): fresh install of 12.04

I have no clue what 1+2 could have in common, despite the fact that
those are the main working machines and 3 is not used that heavy ....
what I wanna tell you is that on 1+2 far more
experimenting/configurations is done while 3 receives clean
configuration solutions after they work on 2 - confused? me too! :D

Hope anything of the above is of at least little help!

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https://bugs.launchpad.net/bugs/494400

Title:
  Opening folder with nautilus-gksu change desktop wallpaper to root one

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