It's the multiplexing coming from the N163 chip. It happens when you have more than six N163 channels enabled. You should notice the difference when you play an N163 sound with six channels or less enabled, and then with seven or more channels enabled.
I hecka love your compositions stewboy. Your education really shines through in the way you construct your movements! I imagine you will end up being a super successful tv/movie/game composer pretty easily with this kind of epic writing.