The file format thing is a known bug that'll be fixed whenever the OP has time to release a new version.
As for the special chip error, that's because Nintendo's built-in SNES emulator doesn't support games, like Kirby Super Star, that used special chips. This won't ever change unless Nintendo releases such a game as 3DS virtual console. Instead, look for the SNES Forwarder Maker, which was made by the same guy that made this fine injector. It LOOKS like virtual console, but it runs on an emulator behind the scenes in an attempt to boost compatibility.