Assistance determining what my Jeep is doing
At the time of this post, your Jeep is sitting in the parking lot NOT moving, from the best I can tell from your post.
Sorry, its probably a bad time to be funny doing the Capt Literal routine, and you're probably NOT in the mood for it at this point either.
This happened on my Chrysler 2002 Mini-Van, and my 2010 Commander has the basically the same system, but it does sound like what your experiencing on your Commander is the same as what happened on my mini-van.
Like dhh3 was saying, on my '02 mini-van the blend doors for the heat/AC control are driven by an electric motor. There are several doors but only one motor, the motor drives all the doors by a series of plastic cams and gears. In my mini-van we had a pencil fall down the Defrost Vent into the heat/AC box. This resulted in the next time we changed the heat/AC mode, we got a loud clicking noise and then the sound of a snapping pencil. BUT the air did NOT flow properly from the vents for the mode that was selected, and everytime we changed the mode, you would get a loud clicking noise, and it never directed the air properly.
I got on the floor of the mini-van and found the motor and plastic cams/gears for the air blend doors. Sure enough, the resistance of the pencil that fell into the air blend doors had causes the plastic gears to skip several teeth and were out of sync, that resulted in the doors moving to the wrong position and some doors hitting the stops before the others and that would cause the plastic cams and gears to pop, skip teeth, etc and make loud popping noises as the motor continued to drive doors that had already hit their stops. I was able to fix it by just forcing the plastic cams and gears back to the proper positions, plastic so there was some give and skipping teeth between gears did no damage. I lubed up the gears with some white lithium grease and its worked fine ever since.
Luckily, on the mini-van the motor and gears were assesible from under the dash and laying on the floor of the vehicle, I had to pull a few trim pieces and it was a tight squeeze for my big hands, but I was able to do it. It might NOT be as easy on the Commander, I have NOT done it on a Commander. When I pulled the trim panels below the steering wheel to wire up my aftermarket gauges, I could see the motor and gears for the Heat/AC blend doors.
If the motor is still clicking away trying to drive an air blend door that is already on its stops, this is what I would try.
1st-Change the mode and temperature of the heat/ac, see if the motor then changes to a position where it does NOT keep trying to drive an air blend door that won't go there, and thus keeps spinning trying to do it and making clicking/popping noises.
2nd-Try turning off the Heat/AC with the power button.
3rd-Try killing power by pulling fuses for the heat/AC system.
Next, if the problem is like I suspect, it might be different, you have to get under the dash and resync those plastic cams and gears, you'll have to force them back to the original position. I'm pretty mechanically inclined and was able to figure out the proper positions by just observing the motor/cams/gears moving for the various modes. Basically drive the motor to one extreme, and you can pretty much figure out where everything should line up, because they should be at their extrem in that directions as well.