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#11
What exactly is the default Factory Recovery you ran? Are you running Factory Recovery from its partition on the HD at boot or from the OS? Or are you running the Disks?
Please fill in your System Specs in bottom left corner of posts.
Do you only have a problem with Shutdown now? If so check your logs and System Resources for clues as to what is hanging Shutdown: troubleshooting steps
If these don't solve it run a Shutdown trace: Gathering a Startup, Shutdown, Sleep, Hibernate, or Reboot Trace - Windows 7 Forums