As for problems with the room keys and RFID, the biggest issue has been bugs in the system where the reservation was downloaded improperly.This happened BEFORE RFID as well but has been more prevalent since the introduction of needing the PIN. Other than that, on the CM end (specifically mine), there has been little to no issues.
As for putting two rooms onto one room key, if it is a reservation setup that way, I'm sure there is a way to do it. I'm not too positive as my resort uses connecting rooms in the instance given (4 people, 2 rooms) and the connecting doors are usually left open. That being said, if it's two separate reservations trying to access each room, again not sure how it would be done as the program only allows for the room on the current reservation to be active.