Could also be the indexing service - runs in the background indexing files on your hard disk to spped up searching, I think.
It can be safely disabled.
Have you got Windows Defender installed? My XP setup every now and then was thrashing the hard drive once the computer was left for a while, It turned up to be Windows Defender scanning the hard drive.
If you're running Vista it's almost certain to be the indexing. I get the same thing when I boot up, hard drive goes nuts for about five minutes. It's a good thng!
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