Quoting Thrax

@ Unregistered Guest (LAAAAAAATE):

This is probably due to some form of interlacing or telecining on your video source. Without a sample of your video, I can't tell you how to proceed. Suffice it to say, a telecined source is a video that blends fields (frames) together in a pattern to ramp the video up to 29.97 frames per second for a projector.. A telecined source displays lines through the picture at fast motion. An interlaced image blends all fields together, and only a thorough/complex deinterlacing engine (Which AutoGK/GK has) can make sense of it. Post a sample, though.. That's the best way to get the issue resolved.

@ Splung:

What's your source?
What program are you using?
What audio type are you using?

Try using Real VNC or Media Player Classic to play the movie.