Does this happen at regular intervals throughout the playback of video? If so, it is the video seeking to a forward location to catch up to where it should be - meaning it is unable to keep up with the playback framerate in normal conditions. If your system specs are semi-decent and you don't think this should be happening, it might be a good idea to check what codec is being used for playback, and maybe experimenting with that (although I've found ffdshow to be perfect on all the test machines I've used).