Comment 2 for bug 438196

After some experimentation, I think I've figured out it's not mplayer itself that causes this.
I've also had similar pauses from vlc and totem which led me to try various settings in compiz without success, then killing compiz.real completely and running mplayer without a window manager.

I had no pauses then, the problem seems to be caused by something odd happening at the window manager level.