1. Are you running NORTON?
Norton is a resource hog...I know there are "believers" out there but that's my experience.
2. Have you run a thorough system scan for viruses etc etc?
You could have all sorts of evil stuff going on that's using your system, are you on-line when this is going on?
3. Have you checked the START UP tab in MSCONFIG (via RUN)?
You could have a lot of programs opening on startup and running in the background. Un-check any you don't need to start running right away and see if that speeds things up.