I definitely agree that the Flash cart caused all of the errors as I've tested several other emulators and flash carts. All which functioned normally with PokeGen. Also during the testing it became apparent that no other file wrote in that group of offsets that were previously mentioned. As for the pc boxes error that I mentioned; that was corrected when the game was beaten and the national pokedex was unlocked. So once again thanks to Codr and Kaphotics!