This is like my 3rd or 4th post where I mention capacitors, but I have to in this case again. The pc downstairs in my house was having a similar problem, then the screen would lock up for like 2 or 3 minutes then go back to being barely usable etc....
The culprit was blown capacitors on the 6200A-LE card which I replaced and everything is fine now. It makes me think your situation might be similar because if the card wasn't being pushed....i.e. vga
driver, it was alright.