Ok I have the downloaded version, I use Pokesav, but the problem is that I am past the Elite Four and I captured Dialga and Palkia but I saved before and every time I save after that save it seems to load the the save right before Dialga and Palkia. Anyone got some answers.
Go to this thread https://www.romulation.org/forum/index.php?topic=16350.0 and find the link to the download, there is a R4 Fixed rom, just rename your existing .sav data and it will work .