We still have this problem.  It is especially apparent for us because we
have 25 machines running folding that students use and sometimes reboot
into Windows. Folding slows the logout process significantly, and during
this time gdm comes back up and you can log in, however, the machine is
still in the process of logging out and when it finishes roughly 90
seconds later it reboots, regardless of whether someone has logged in or
not.

It seems to me the problem is caused by killing gdm on logout instead of
stopping it.

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gdm spawns a new X server when told to restart the system
https://bugs.launchpad.net/bugs/126797
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