Computer Stutters????????

Basically this started about a week ago. I was installing this whole batch of windows updates and it finished and told me to restart my computer to finish installing them. However I was in a game of Starcraft 2 so I waited to restart. Well I forgot to restart it and about an hour later the audio would stutter then basically my mouse and video. (Basically the computer) So I restarted it to finish installing the updates. Well it is still doing the stutter. I thought it was skype at first because whenever I click call or send a message it would happen 1/10 times. It is happening now just having a song in the background. Maybe every hour or so it will happen. It lasts about 2 seconds then goes back to normal. I have updated all my drivers and checked for viruses with multiple scanners and there are none. Anybody know how to fix this stutter?