OK... I checked mine today, to see if I could narrow down my clicking noise..
It's a cold day today, slightly rainy. If I press "up" on 20 degrees, I hear the actuator move a little, and the air feels warmer. Each time I push it up I hear another little actuator movement, and the air gets consistently warmer until about 30 degrees... my motor was still warming up at that stage.
So... based on that, i'd say you may have a problem. I tested using the blower on "face", outside air (not recirculated) and no A/C. Tested on fan speed 1 and 2.
AND! My clicking only occurs when I turn the car on, or after that, only when I choose "feet". All the other vents switch smoothly and quietly. (gotta find that other thread now!)