I didn't mark it as solved. It just popped up and I can't seem to get rid of it. Sorry.
Also I do know about the upgrade process requirement of restarting. The upgrade process is done. My PC will not shut down without holding the power button.
There maybe some hardware device that doesn't have permission to let Windows shut it down.
Leading candidates might be the Firewire/IEEE1394 or USB controllers.
From the Start menu, use the search bar at the bottom and type in device.
And choose Device Manager from the list of options.
Find the Firewire and USB host controller entries and open the category (the little triangle). to get the list of devices,
Double click on the device and make sure the box is checked that says "Allow the computer to turn off this device"