Hmm. I've never played the game, but the guitar might be clipping. It's not related to the pitch issue, else it would sound just fine on the CM-32L.
Well I've uploaded the CM-32L and MT-32 versions. The part where the CM-32L crackles is at around 1:40.
CM-32L (Done by Talus on Kohina)
MT-32I haven't a clue if it is clipping or not, if it was, I would have expected other parts of the music to clip too.