I see you mention it does this for hours, this is very strange as the initial disk activity at boot shouldn't last longer than 5 minutes, usually it's less than that.
Have you tried disabling the other things i mentioned like SuperFetch ? I don't really believe that is the problem here but it's better we try it just to make sure. I suspect some third party program is creating an issue here but i am just guessing.
Can you tell us which programs you have running in the background(like virus scanners, firewalls, anti-spyware etc.) ?
Also can you go to Task Manager - Performance - Resource Monitor and click the Disk tab. See which process is creating the most disk activity, this should help us narrow it down ...
Cheers !
Mikey