Tried your rom out, still blinks in battle. Also, the game seems to freeze up when I try to leave the Black Bird (after getting all my swag back, you know)
Judging by the posts, it's sounding too much like an emulator problem, and not a rom problem. Try bsnes, Snes9x (current and older versions), and Zsnes (current and older versions). If it happens on bsnes, then that's how it would perform on the hardware. As a result, you'll need to rely on the less accurate emulators for it to be correct.
And likewise, if bsnes doesn't display the errors, then it's the crap emulators (Snes9x and/or Zsnes) that are the problem. Since the core has had so many changes, you'll probably want to ask what the others here are using to get an idea of what to use.