hmmm this might make no sense whatsoever but here it goes.
think of it like shaving. when you faro cards there is a "grain" depending on the cut. traditional cut makes it so the cards never get "razor burn" from "shaving" (faroing) either direction. so non-traditionally cut cards get "razor burn" or don't faro when you go against the grain of the cut.
this is all assuming that you aren't just forcing the cards to faro when they don't want to. it should come very easy, like a key and its corresponding lock.
i have no expertise in this field at all. this is just an observation. PLEASE if someone actually knows a better, non-stupid explanation, like mine, to explain this please share.
(just to be clear i am saying my explanation was stupid.)