Saw a series of solutions for this problem (including mine) on another site. This may solve your problem as well.
In Device Manager, a number of devices may show the "Power Management" tab with the "allow the computer to turn off this device to save power" box checked.
===> If Power Management tab is present, UN-CHECK the "allow computer to turn off this device to save power" option.
In particular, I saw this same recommendation for (1) M-audio sound card, (2) IEEE 1394 controller, either built-in or on other hardware such as Creative Audigy sound cards, (3) LAN network adapter, and (4) USB Root Hub... which was my own particular solution (I have eight of these on my motherboard, and I un-checked the power save option on all eight).
Once these power save options were un-checked (just the USB ones, for me) lo and behold Win7 Pro 64-bit would now shut down normally.
Obviously this is a Win7 bug, and hopefully it will be fixed by MS eventually.
Or, it may be tied to BIOS settings. I certainly have not changed any default Power Management settings for my SuperMicro C2SBX board, but it shuts down fine under WinXP Pro. Just not under Win7... until I un-checked the options on USB Root Hub as described above.
