I can confirm this bug on Ubuntu 11.10.

I am using:
GNOME Shell 3.2.2.1
GNOME nautilus 3.2.1

Some more information about this bug:

It occurs whether starting nautilus from the dash (or panel or whatever
it's called in the activities overview), or if I start it using  the
keyboard shortcut that I defined for 'Home folder' under 'Keyboard' in
System Settings. It does not occur if I start nautilus using the run
command prompt (Alt+F2).

Nautilus will reappear for me (sometimes) if I switch to VirtualBox (in
fullscreen mode), escape, and alt-tab back to an Ubuntu window. Upon the
next alt-tab, it will be in the list. Note: this doesn't always occur
however, and sometimes I have to repeat this process multiple times to
get nautilus to appear in the alt-tab list. On second examination, I'm
not sure if this is related, but it is happening multiple times.

Please let me know if I can be of any more help.

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https://bugs.launchpad.net/bugs/971715

Title:
  Nautilus doesn't show up in alt-tab in GNOME 3

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