As suggested in the bug description, this bug still exists upstream in kernel 
3.1. However it appears to be fixed upstream in 3.2-rc1:
http://kernel.ubuntu.com/~kernel-ppa/mainline/v3.2-rc1-oneiric/

** Tags added: kernel-fixed-upstream-v3.2-rc1

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https://bugs.launchpad.net/bugs/768039

Title:
  Optiplex 990 fails to reboot/shutdown

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