I posted this in the comments where Andywinxp posted about his iMuse fixes but it ocurred to me that article is too old for people to go back to and see, so I'm posting it here.
"So I've done some more testing, and there seems to be a bug in the music. Sometimes, when the music is transitioning from one track to another, the previous track continues to play, or it transitions to the start of the next song rather than whatever the track's up to. For example, in the Barbery Coast, when you finish talking to one Rottingham, it transitions to the main theme but keeps playing the Rottingham version. I also noticed that when Guybrush comes back from the Plunder beach to the Voodoo Lady's after finding Elaine's been kidnapped, it keeps playing the generic Plunder beach theme over the top of the Voodoo Lady's theme. This seems to only happen when you've been playing the game from the start, as I've tested it using a save and it doesn't happen. I don't know how many other times this may occur as I didn't get that far but it seems like there might just be a bug in the fix that needs to be ironed out."