The first is most likely correct. The second implies that both PokeGen and the patched ROM are reading it wrong, which is not that likely, as both of them read everything else correctly.
Ps.: Btw, I use the .sav file on a japanese ROM when doing anything like EV training or cloning. Just to be sure.
Ps.: Btw, I use the .sav file on a japanese ROM when doing anything like EV training or cloning. Just to be sure.