Major bump, but I was just wondering if anyone happened to be looking into this behavior over the last few years.
I can confirm that it's localized to specific games, so it's probably not an issue with USF or currently ripped sets as a whole. Here are some games I know of that definitely have the behavior:
Super Mario 64 Mario Kart 64 Star Fox 64 The Legend of Zelda: Ocarina of Time The Legend of Zelda: Majora's Mask
These are all Nintendo titles. It also seems that HAL's games do not have the behavior. These definitely don't have it:
Super Smash Bros. Kirby 64: The Crystal Shards Pokemon Stadium Pokemon Stadium 2
Do certain Nintendo 64 games use specific "sound drivers" like SNES and Mega Drive games do? This selection of games might have something to do with that, especially since the games affected are all Nintendo titles.