Thanks a lot, this actually does give me a couple of possibilities and I may even be able to recreate it manually. My guesses are either the audio thread is sleeping too often or I'm not judging latency properly for all sound cards. I thought it might be just the vorbis streaming not working correctly from the longer loops but I hear distortion on the plasmagun's shots as well so it would have to be a problem with the overall audio. Either way this gives me a good idea of what might be wrong as its similar to problems I've already had.
I'd have replied much sooner but itch appears to have swallowed up the notification from this reply so I didn't see it until now!