Cetain applications working slow

I have had my computer for about a year. It has worked fairly well.
A few days ago I noticed while working in Autocad, the cursor would
start moving really slow. Other applications worked regular speed. I
brought up TV on media center and it too moves real slow. I think the
problem started when I tried to watch Hero's on NBC website. If I leave
the computer for a while and then come back these applications will be
fine for a while but then the slow bug kicks in again. I have
uninstalled my graphics driver and rebooted, didn't work. When I cold
boot, it works for a couple of minutes. Also, I can hear my computer
working nonstop. Please help, I need to get back to work