Have you compared part numbers of the old and replacement CCU?
I can't remember exactly, but I'm sure the CCU has something to do with the immobiliser and alarm system, presumably it'll pass the key recognition code to the alarm module, and send the vehicle unlocked command to the alarm too. Normally when the CCU is swapped, it's best to swap the alarm module and ECM at the same time. There are sellers on ebay that sell kits of everything needed, often including a fob or two in the kit.
Using the door key all the time isn't ideal, as the lock is designed for emergency use, so they wear and fail eventually.