I cracked the PCNYabcd algorithm! It uses a variation of BACD algorithm with unrestricted seeds. PIDH is xor'd against PIDL, TID, and SID.
This algorithm makes antishiny detection easier (PIDH is less than 8 before alterations) and presumably if the pokemon becomes shiny, it could be easily modified. I don't have any specimens that require antishiny though.
A few factors prevented this from being detected earlier. Mainly it was a bug in my check code from 2013. The check code didn't matter prior though cause it turns out almost all of the PCNY I received from people were hacks. The pokemon from Pokemon Secure are mostly hacks too.
And of course the pokemon from GameFAQs on the box save are all completely legit. This is despite Pokemon Secure and others saying they werent.