From the tests I made, it really looks like the problem is not in the game, but in KFF (that's why I opened the issue of KFF's GitHub). Unfortunately, there hasn't been any reply yet, nor have I received any feedback from EF owners, so I still don't know for sure.
That said, if you send me an email from the same address you purchased the game from and tell me which zone you reached, I can send you a cartridge image which will allow you to start from there.