I'm just pulling things out of the air. These are my first thoughts...
Swap the vid card, leave ALL ELSE the same. Do it 1 piece at a time, so you know it was only that piece. I.E if you swap card and change connection at same time and it fixes it, you know it was one of the two, but not which one. So 1 at a time try swapping card, the way it's connected to the internet, pull 1 stick of ram, then pull the other stick of ram (having it not show up makes me worry about bad RAM).
If it's not hardware itself (that is, if you try all this and it still has the problem) then it's a software problem. It might be vid drivers, but not likely. If you swap the vid card this should go away. If it remains with the other vid card it won't be the driver (I don't think).
The last remaining problem is probably a service, setting, or configuration inside Vista itself. This is the toughest to weed out, as it could be so many things. It could be the simplest of processes that just runs a check for peripherals every 3 seconds (for just one example). Hell I once had rhythmic lag spike because my printer was off and shared, and somebody sent a print batch to it. It kept checking over and over to see when the printer was back online. Pretty messed up stuff.
Skuzzy's been doing a lot with Vista lately (much to his loathing). Perhaps calling him on the phone and having him run you through some of the most likely services/processes would be the most time-efficient method. The other method involves doing massive amounts of internet searching and problem solving.