Thanks a lot for the update. Considering that I am out of warranty, I hope it does not get worse in my car to more than the gear noise.
I bought my car a year ago and the noise started a couple of months ago. I don't have any air flow issues, but I have a weird symptom since buying my car. When I start the car, warm/hot air would come out from the vents for may be 10 seconds as if the heater is on. It then changes to cooler air.
This may have something to do with the flap not closing so some hot air from engine gets initially in the car. Don't know. AC and heater function OK with the exception of the noise!!