The English versions of the games haven't been tested with PokeGen at all, at least not by me. Usually there isn't enough of a difference in the save file to make anything break, but there could be. Don't bother uploading the .pkm files though, as that's not going to provide any useful information. As for what the problem is, I don't know, and am not going to try to offer support for the English games yet. If I had to guess, I'd say it sounds like you used the wrong target game settings, or loaded the save file itself as the wrong game.