The problem is related to the emulator core/audio timing of the emulator. The game uses a special sound system (MusyX), which can be difficult to emulate. PJ64 1.6 has problems with this system, so its not really a problem that the end-user can fix with just the default settings in Project64. However, the current beta (requires a donation for access), I believe, has this sound problem with TWINE fixed.