Well there's certainly a quick way to check. If you're correct (and I'm starting to suspect you are), it looks like Blondbeard's FullMonkeyMap is the one from CD2. Blondbeard, if you copy the file MonkeyData\Textures\FullMonkeyMap.imt from CD #1 over top of the one you have, do you get music at the beginning?
Obviously, I need a way to stitch together the two files (which dovetails into another feature I was planning anyways), but for now that would at least get you music in the first half (and confirm our theory).