Zsnes ftw! I don't really hear the glitches in the snes9x one, but bizhawk (the most "accurate emulator") I hear them obviously. I'd like to figure this issue out as well and have no idea what causes it other than it seems to be emulator related, meaning one would have to edit the emulator and not the song/rom. Retron 5 I'm fairly sure isn't "real hardware" since it is using emulators as well, I think snes9x for the snes one? I'd be willing to bet the songs would work on a real snes. But have you tried putting another song in the same place to test if it is the song that is causing the sound glitching? Or does the song work in normal addresses? I've been to lazy to test this with my glitchy songs...
We are born, live, die and then do the same thing over again.