I think I might have found something worth looking in to. I'm sure we're all familiar with how CatSFC sacrifices sound accuracy for speed, and how it produces sound/music that is higher pitched than normal.
Here's the strange thing: if I load Secret of Mana first, and then, without closing the content or exiting the emulator, load another game, the sound issue appears to be fixed. However, if I load a game other than Secret of Mana first, or close SoM completely before loading another game, I'll get the high pitched sound again.
For some reason, I always seem to get accurate sound from Secret of Mana, and that apparently carries over to the second game I load.
Strange workaround, but I've been able to reproduce it several times.
I am using the CIA build of CatSFC as it is available at this time.