Hmmm, maybe spyware (and similar dirty stuff) is slowing down the PC. I don't know, but it seems like something I've encountered myself before as well when I read your explanations.

Maybe the harddisk is too fragmented? Even then, it'd seem unlikely that it could be so slow.

Do you notice anything about the physical CD/DVD drive?

Maybe you need to update the motherboard BIOS?

I think more information is needed :)