Try using the resource monitor and see what is actually using the HDD like that. You can get there from the performance tab on task manager.
This will show what is actually using the HDD. It could be used heavily for swap (as Ironsounds said above), could be windows is stuck in a loop while trying to index it (speeds up searching), could be windows defragmenter is using it (and is stuck in a loop hence never completing).
Lots of things can do it, the disk tab on the resource monitor will at least tell you what application is at fault - and from there can offer better advice.