The movie config layer is not active for recording, only playback. Thus, recording ends up stuck with default SYSCONF settings.
The fix is simply to add in the movie config layer when recording. The way it's done is a bit hacky, but seems to work.
This should reduce (but not completely eliminate) gradual audio desyncs in dumps. This also allows for accurate sample rates for the GameCube.
Completely eliminating gradual audio desyncs will require resampling to an integer sample rate, as nothing seems to support a non-integer sample rate.
CasualPokePlayer