two things could be doing this
Are you encoding the at the right bitrate? Some DVD players are more forgiving than others at slightly odd bitrates (whereas your computer dosn't really care). Off the top of my head I can't remember the correst bitrate, but a quick search on either the transcoding forum or Google should give you the answer.
Are you using a re-writable disc? From personal experience, all 3 of my DVD players (well 2 players and a PS2) give strange "side effects" when on a re-writable, but fine on a DVD-ROM.
Good luck in finding the problem, and if you do find out, please write and let us know what it is.