Alarm problem after ignition switch change

What is your question?

Hi, I have a 2006 Jeep commander. Dealer replaced switch and afterwards the alarm would sound a couple short beeps AFTER I locked the doors with key pod. Then key pod would not unlock the doors so I manually unlocked them and they would automatically lock before I could even grab the door handle to open it? Then it started sounding every time you unlocked the doors with key pod and will not stop until you crank it. I carried it back to dealer and they are telling me it is the keys? They can not program the keys to the jeep? It is the original keys for the jeep? I told them it started this after they replace the ignition switch. Now they are telling me it is the driver door lock acrator? None of this started until they replaced the switch?? Please help.