Some MP4's play choppy vid

OK, I searched and couldn't really find a similar issue, so here goes.

Caveat: I am new to apple products so bear with me...

I wanted to get some of my mp4's from my home server onto the iPad for my son to watch on an upcoming cross country flight, well I found that I needed to download iTunes to one on my PC's then connect the iPad and then just move the videos that way however one of his favorite video's will not play properly with the apple players.

I moved about a dozen full length movies, and 1 doesn't play correctly. The sound works fine and there is no choppiness there; however the video quality is very choppy and almost nauseating to watch. I play that same video over my media server to my TV it is OK, if I play that same video on the PC I downloaded iTunes on it plays OK in media player, but in iTunes it is just as choppy as it is on the iPad. Is there anything I can do to this video to allow it to play correctly on the apple players?

Thanks,
John