If you can get as far as 'shutting down', it may not be a problem with viruses, rather with power down issues. The OS is unable to signal the hardware to power down the computer, although it is done with OS part. If your system reaches 'shutting down', it should not be performing any hard disk operations.

Does this happen everytime you shut down, or just sometime?

I suggest you to repair your registry. It resolves most of the "Windows" issues. (I use/recommend ccleaner).

If the problem still persist, update your BIOS and check if you have any 3rd party power management software installed. Here's the details:
http://support.microsoft.com/kb/927393/en-us

Please post the results after you follow these steps.

11D.