Hm well I used a save file that bond697 fixed for me but I had to go in their to change levels and abilities. Nothing else was changed but I wasn't allowed back in. The last reply I got from him was this.
"nothing looks wrong at first glance, but something is definitely screwed up. pokegen won't allow more than 8 chars for nicknames+trash bytes in your save while the actual nick+trash total should be 11."
So Im stuck for now wondering why my pokegen is messed up even after I re downloaded a clean pokegen