I'm not saying the game is a jerk or anything weird... this is likely to be a graphical issue.

When I play in windowed mode, the game tends to hang every other minute for a second or two. It doesn't really kill me, but it's very annoying. What's the issue?

I'm using an Nvidia 9600 GT and my processor is an Anthlon II 64 620 2.6GHZ 2MB AM3

I updated my driver recently, but didn't do a clean install. Could that be the cause too?

By the way, I have no problems running a very high res and modded skyrim.