Do you mean you get a slight "delay" or "skip" in your frame rate?
Because i'm having the same problem. I can also see it when i run
glxgears, looking closely at the gears moving, every few seconds
i see a slight 'skip' in the animation. It happens in all my OpenGL games.
I found that i can fix the problem by modifying my XF86Config and
removing some of the loadable modules.