The problems come from the fact that the resort front desks, which create room keys, use a different computer nework from the Guest Relations windows at the parks, where you get APs. Cross-connecting those two systems is a royal pain for the GR windows.
But there is a simple way to do it that some on the boards have used.
At time of check-in, don't let the CM code your passes onto your room keys. They can give you a completely separate card that ONLY has your ticket on it.
Since the card ONLY has a ticket on it, it does not require the GR window to access the resorts computer system, only the ticketing computer system, which makes the whole process go much smoother.