Hm, that's kinda weird. My WSMKR Jirachi, while not shiny, made it through the hack check. Don't see why a shiny one wouldn't make it through....especially since Jirachi aint shiny-locked.
And because I misinterpreted the actual topic: I'm kinda glad that PokeBank's hack check is the way it is (minus the part where it prevents legit pokes from making it through). It usually prevents the really obvious hacks from making it through (Wondertombs, Magikarps with Dark Void, etc), but still allows legal hacked pokes through. I had Pokegen'd or something a few Pokémon that I like with some perfect IVs and the right natures, moves etc, and fiddled with my Zekrom's IVs, and was afraid that they wouldn't make it through. But they made it, and all is good.