I've had this same problem for a while as well, using Compiz Fusion. First there were flashes of black frames and black checkerboard patterns, then with the 180 series it changed to red frames and red checkerboard pattern.
I'm only running mplayer, no amarok, etc. and the only solution I've found is to quit and rerun mplayer until the flashes drop to a frequency where the video is somewhat watchable. Seems to be something to do with redirecting the video overlay to an OpenGL texture.
Running an 8600GT.