Ah, so it's a known bug. That certainly explains it as I was using v1.0
It would be great if you could fix the file... but only if it doesn't take too long. I wouldn't want to rob you of precious time that could be used to improve the emulator further. I'm sure the community would have you work on that rather than fixing some dude's 3dn file for an obscure version of a popular game.
That said, if you can fix the file and it meets the required quality standards, I would be happy to submit it to the repository :)