Shutdown works on a software level (the OS shuts down properly), but the machine doesn't finish and the fan still runs and the power light is still on. Is there a setting I need to modify for the machine to shut down correctly?
From a comment here (http://www.jamespaulp.us/?p=235):
Here’s the solution!
Click “Start”, on “Computer” click right mouse button and select “Properties”, click “Device Manager”, select “IEEE 1394 Bus Host Controllers” group, only contains one device called “VIA 1394 OHCI Compilant Host COntroller” on that click right mouse button and select “Properties”, select “Power Management” tab, and finally check the “Allow the computer to tur off this device to save power” box! That’s all folks. After that the computer power down normally every time.
Windows 7 RTM isn't really accessibly until August 6th. I'd uninstall the copy you used as it is probably not really RTM.