If you use JFugue, it's possible that you've come across a bug where JFugue's Player.play() method stops play after it is called around 17 times. Brian Tarbox and I have been trying hard to track this one down... and we think the problem lies within the javax.sound.midi code.
It seems that Java's Sequencer.open() and Sequencer.close() methods might be happening asynchronously. As we were debugging this, we found that we'd get an IllegalArgumentException from a Sequencer that should have just been opened. It's possible that it was opened, but then the close() that was called shortly beforehand might have finally taken affect.
The bug is Issue 49 on Google Code, in case anyone would like to lend a hand!