I have had buffer underruns, but only with FLAC, and only certain points in certain songs (though it'll do it at these points consistently.) It seems to have to do with the fact that they're VBR so it can't properly predict when there's only 5 seconds of song left in the compressed buffer. At least that's my current guess, and I've been told in response there are issues with VBR code.
Setting the anti-skip buffer from 5 to 15, or turning off disk power down, both fix the problems.