Running 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.
Try to use gksudo -- nautilus --no-desktop instead.
The -- tells gksudo not to parse the remainder of the command line.
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