Hour-long shutdown duration "shutting down hyper-v virtual machine management service"

The hotfix in Microsoft KB2263829 might solve this problem.

It sounds like some kind of serious glitch occured. At this point, a hard reboot is probably your only option.

As a side note, make sure you upgrade your BIOS to the latest revision (for microcode updates), and make sure the needed virtualization exetnsions are turned on. Same goes for drivers, particularly the drivers and firmware for your RAID controller and hard drives. And running a chkdsk /f wouldn't hurt either.

Are you running any other applications on the hyper-v host? I've seen this type of issue when there has been AV running on the host.