It's normal. When you launch Nautilus as root without the option --no-
desktop, this new nautilus instance begins to manage the desktop. You
just have to launch gksudo nautilus --no-desktop.

-- 
Opening folder with nautilus-gksu change desktop wallpaper to root one
https://bugs.launchpad.net/bugs/494400
You received this bug notification because you are a member of Registry
Administrators, which is the registrant for GKSu.

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