ReCast FF3: War of the Magitek

The invisible status monster has a script that tells it to self-terminate once it detects no other enemies on the field. It has the fastest speed possible, but it still has to wait for its turn in the que. Try waiting just a little longer, you can even use the extra time to sneak in a healing spell before battle ends if you're swift.

If that doesn't work, could you tell me which emulator you're using? I tested the hack in SNES9X, maybe there's an emulator-specific bug.

EDIT: Oh wait, I had to add something that would stop the status monster from casting spells before "MMMMMMMMAGIC?!" plays out, because it was triggering the cutscene. I'll look at the script, maybe that's the problem.

EDIT post V1.01: Yep, that was the problem. The monster was stopping itself before it could destroy itself. Dang, I played through the opening like thirty times, how did I miss that? You can cast a spell during battle to fix this in the current version (even if all the enemies are gone), and the bug is fixed in V1.01 provided you don't load a battle savestate (since the script in progress was changed and would probably crash the game).