The problem with that is I'd have to make a new installer each time I make a new patch, and with how often I make new patches for the game, that'd get really tedious (hence why I don't do it that way. That, and I know that most people don't want to fiddle with installing the game on their computer and whatnot). Still, that's really weird that happens. Ok, some questions to see if I can't discern where this stems from:
1) Does this happen after battles for maps?
2) Does this happen when transitioning between areas?
3) If yes to the above, does this happen if you go back and forth between rooms?
The one for battle makes absolutely no sense as again, I've never heard of this issue with battle music seeing as regardless of the music choice, it should be working flawlessly...
It's manual, you have to go into the menu after stepping on one to save (you can also save on the world map, same thing there).