I'm developing a game using J2ME (and it's game API) and I'm playing some music, a midi, using the MediaPlayer however the sound is coming out extremely choppy. If I comment out the rendering code it plays normal however. I've tried creating / starting the player in a new thread with the same result. There must be some trick here as all I have to do is flip the buffers every frame for the sound to break up.

Did you try limiting framerate? Like fliiping the buffers once every 1/30'th of a second? It's possible it takes all CPU time which doesn't allow the midi to be processed.