Door Actuator

So just recently I have had two blend door actuators replaced. The first one I had replaced was the defrost blend door. Seems to be working fine. Second one I've had replaced was the air flow blend door and as of the last two days the AC/heater/defrost has been randomly not working for long periods of a time. As soon as it comes on it cuts in and out. Then just out of no where the most recent air flow actuator is clicking from behind my steering wheel every couple of seconds. I am not sure what is going on with it. I herd someone say you have to time them when you replace blend doors. I am not sure what that means. Please help.