My computer keeps lagging every 20 minutes?

So i'm watching a movie and evey 20 minutes my computer is lagging bad and i see the red light on the front case lighting up full, but when I move my mouse it stops. Please don't suggest it's a virus as I'm a blackhat myself. I've changed my poweroptions to go into sleep mode or monitor to turn off to never and I've closed down everything non-related to my movie. And it's not like this computer to lag as it's a quad core Anthlon. I can run the most recent video game on max settings and I wont lag.