Even shitty hacks don't inherently corrupt a save file. PokeGen isn't responsible for this, and this isn't the right section anyway.
My hunch would be you purchased a bootleg.
Either way, this isn't the proper place. "Site discussion" is for site discussion, not discussing how you screwed your save file.
On that note, if your save file or game cart is messed up, there's nothing anyone here can magically do. But thousands have used PokeGen without screwing up their saves, so I doubt it is the source of your problem.