Originally Posted by X Marks The Spot
The only thing I can think of that comes close to what you're describing is automated updates or a virus.
Nah, auto update would give several visual cues, plus restart the computer.
On topic: This sounds like a number of things, from a faulty gfx card, insufficient power and overheating (are you overclocking?). I'd check temps first:
For graphics cards - search for GPU temp
For CPU - search for alcpu
Sorry for lack of links. Apparently you need 10 posts to link anything. Lovely.
Post the results (along with the processor you use) here.