So the AddMusic by Perl tool is officially a bit outdated now and certain music doesn't work with it? Thanks, that might explain why certain tracks don't seem to be working correctly.
But a quick report would say that a big example of music that doesn't work for me without removing a whole line is the Mario and Luigi Bowser's Inside Story final boss music. It says there's a syntax error on a certain line, although removing that makes it play nearly well after being added with the AddMusic version I'm using.
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As for Mario's Nightmare Quest? Well, it's currently on Fusion Gameworks, ROM Hacking.net or the GCN at the moment.