Video playback can be a bit strange at times and mostly it's down to the way in which codecs are interpreted.
I take it we're talking windows here? I found in windows WMV's at the most compatible and will always work on the platform although of course not an ideal format. Make sure you set video dimensions correctly and it's also worth trying to stop the video and then sync and play it again just to see if that makes a difference. Also are you using any touch commands as these (I've learnt) can throw in some issues if the syncing and timing isn't right. Maybe set a delay from touching to stopping and playing the video.
Another annoying issue with videos is the Gamma mac issue. If you play a video on mac the colours can change significantly depending on how you have your monitor calibrated. Why apple haven't addressed this is beyond me and any mac video application that uses quicktime will have this problem so all videos are not played equally.
If it's not broken don't keep trying to fix it.
