Yes, there are weird sound bugs (extended notes, short notes and deleted notes) even with the best audio syncing option in the Snes9x core. I have noticed this, but don't know exactly what happens.
My first guess is that the audio buffer is sometimes getting refilled at the start and end of the same frame (lengthening notes) and the next time is at the start of the second next frame, skipping one (shortening notes, or deleting those shorter than a frame - which I assume the mushroom sound is using).
My second guess is a data race between the audio thread and the Snes9x core, which gets me sound for a SNES state that is still advancing between the start and the end of my request.
If neither of those is it, I'd have to get recordings from you on Snes9x/PC and PocketSNES/GCW0 and zoom them in Audacity. On OpenDingux you can apparently use 'arecord' (ALSA record), but I don't know if that captures the speaker output or records from the microphone. On Windows you could use Stereo Mix recording. Would that be alright with you?