Sorry, I had a headache last night, and posted the wrong address. I triggered it in Geiger's SNES9x, but the error was at $CC/45A4. The code I'm seeing is waiting on $7E:2143, instead of the APU register.
My save was copied from an unaltered Chrono Trigger ROM - It worked well enough for loading the End of Time for testing, but someone else can probably provide a better one.
In certain locations, opening the exchange menu will cause the glitch. Proto Dome works, at least when arriving by gate. It has to do with the palettes loading in that location, some of which carry over from old location.