I was told that if my computer appeared to be busy when it should be doing not a lot, to suspect a trojan. I have also heard of PCs being partially taken over, and used to send out spam the owner knows nothing about.
Not that I am qualified to say if it sounds like either of those things, however I would be suspicious if it happened to me.
One thing does occur to me though, if your drive is fragmented then the PC may have to work harder to find files. So have you defragged recently?
Giok