I see the "Square sound rape" has been mentioned before. I've been playing through Chrono Trigger with the November 9th WIP, and noticed something... The "monster scream" sound in that game is a well-known example of the issue. In Truce Canyon, 600 AD, if you fight the little green fellows near the bottom, the monster sound before you fight the battle seems to be there, hardly different from the original game...whereas in most other places, I just hear the high-pitched wail, and not the rest of that distorted sound. The only explanation I could come up with (as I'm not exactly a programming guru) was that in that area of the game, there is not really music, just a bit of waterfall background sound (which is still a little messed up strangely, just as in the Heckran Cave). I don't know too much about how the SNES sound worked, but if it's anything like MIDI, then it would seem to me that with music and all, there usually aren't enough channels available to play the sounds necessary to make that "monster growl." Anyway, if that brings about any help, great, if not, ignore me.
EDIT: Scratch that...I just got the working monster scream at the top of the Denadoro Mountains as well...with music in the background... But it's not just random because the enemy in Truce Canyon still sounds the same pretty regularly... Well I'm at a loss then
...wonder why it's intermittent though...