Okay, my findings:
1) Saving and loading the state does NOT fix the problem
2) Doing a save state, shutting down the emulator, and loading that state doesn't fix it either
3) This happens with the LLE interpreter
4) This would probably happen with any game with any DSP plugin
5) The audio gets messed up after the DSP plugin pushes the audio to the mixer
I had Dolphin dump the audio as it was coming out of the DSP plugin, and at it's normal spot. There was absolutely nothing wrong with the audio as it came from the DSP, but there was the issue in the final output.
Image of the issue on a sine wave:
1) Saving and loading the state does NOT fix the problem
2) Doing a save state, shutting down the emulator, and loading that state doesn't fix it either
3) This happens with the LLE interpreter
4) This would probably happen with any game with any DSP plugin
5) The audio gets messed up after the DSP plugin pushes the audio to the mixer
I had Dolphin dump the audio as it was coming out of the DSP plugin, and at it's normal spot. There was absolutely nothing wrong with the audio as it came from the DSP, but there was the issue in the final output.
Image of the issue on a sine wave:
Spoiler: