The only way to fix this is to re-encode the problem videos with settings that allow for shorter distances between keyframes. If it isn't causing you any issues while playing, then it probably isn't too important. It only becomes a problem when you cue into an area that has a large keyframe distance, or if you're playing backwards through such an area (though, it might not be an issue if you've just played over that part of the video, and have your cache size set high in the MixEmergency preferences).
