Pretty sure this has been brought up before, but for one reason or another, there are a few games that suffer from audio skipping/crackling despite having excellent an excellent framerate. Take for instance, Goemon's Great Adventure (U)[!], the game runs full speed 100% never slowing down once, and yet, the audio will skip every two or so seconds. This could be in part due to the way PJ64 handles the RSP emulation, having very poor audio timing altogether. I recall using this version in the past and not having the issues I'm experiencing now. Other games suffer too, like Hybrid Heaven (runs full speed, but every thirty seconds, the game itself will skip for half a second, and continue). Sync game to audio is indeed enabled.
Emulator settings are set to default.
I would post pictures, but it won't let me link them (don't have permission apparently), so....there you have it.