It's made for one specific sound engine. Granted, it's the one engine that 90% of GBA games use, but still, only that one specific sound engine.
Obviously it won't work on emulated games, so that knocks off the first 4. You can get NSFs or GBSs of those anyway.
But having problems with Metroid Fusion and Zero Mission is very strange. I'm pretty sure they used Nintendo's music library, but maybe they don't. Saptapper can't rip them either.