Ohno!
After checking it out on my end, it seems the way the Windows version was originally built needs an update and a rebuild. I was still able to play the game normally after telling the warning message "OK", though, and using the Z key to navigate the menus. If it still causes issues, I'd definitely recommend using a Game Boy emulator like Gambatte or Sameboy to play the rom!
I'll keep looking into it as I work on an update to the game soon. Thanks for letting me know!