It was a long time ago, but I believe the issue was probably either a cheat or a modified rom. I couldn't resolve it so I just gave up.
From what I remember all I did was catch a pokemon then modify that pokemon (so the IVs and Nature would carry over) to be a Torchic. Its been a while since i touched roms and PKHeX, so I don't remember the details. This just popped up in my email so I thought I'd check and see if I can help.