gksudo nautilus in the GNOME Shell changes my wallpaper from the GNOME 3 Stripes background to Ubuntu's warty final default background. I'm pretty sure this is related to root nautilus managing the desktop, but since I've recently upgraded from 10.04 and skipped 11.04, I'm unsure about what GNOME uses for settings now between dconf, gconf, etc, so I don't know where I can edit the setting to stop this. Any help would much appreciated.
I was having the same problem, then remembered that I had installed the "Extended Places Indicator Extension." This extension has the option "Open File System as Root," which I can confirm doesn't mess with the wallpaper. Very nice extension with lots of other useful features.