Some questions

I'm having a hard time figuring out the problem. Maybe the culprit is code at C0/034E. This seems to load a song for the map (presumably after battle). Maybe C0/0358 condition expect a 00 in $053C as silence then with FF condition fails (like if it was a regular song) so it stores FF a song to play instead of skipping the code like 00 would do.

I'd have to do debugging to have a better idea. Maybe try 00 at C2/BF3B instead? Maybe this won't change anything either but it worth a try.