You are correct. There are 2 motors for the dual climate control. One can be reached behind the glove box by removing the glove box. The passenger side motor is on the other side, the engine side of the box containing the blend doors. You cant get to this motor without removing the whole dashboard. Unless someone knows a way.
It sounds like the flap you checked. The drivers side is ok. The passanger side however may be broke. The only way to see this is by cutting a hole in the casing to get access to both flaps.
It is rare these motors break. The blend door spindles usually break first. I think that is the problem the motors are too powerful and carrying out a calibration check each time you start and stop the jeep eventually breaks the flap spindle. Well. First the stop pin breaks that tells the motor where to stop. Once the stop pin has broke the full force of the motor is exerted on the flap spindle. Which doesnt last long.
If its the passanger side flap thats broke and both motors are ok you can buy a replacement dual flap kit
If the pasenger side motor has broken you can buy a single flap kit where the 2 flaps are connected and both work off the drivers side motor behind the glove box. Downside you do loose the dual climate control. The drivers side controll knob controlls both sides.
Your motor may be ok but the passenger side flap may be broke.
I bought a dual flap replacement and went in by cutting a hole behind the glovebox to get to the flaps.
I found 2 broken flaps and a broke passanger side motor I couldnt replace. So I joined my flaps together now they both work off the one motor.
Its held up for 12 months so far with no probs.
When it was on its way out mine made some wierd clicking and creaking noises before it went quiet. The guys above are right them noises 10 seconds after you turn the jeep off are normal. If theres no noise you have a prob.
Oh after fitting the blend door kit there is a calibration check you have to do first time you turn on your jeep to check it. If you dont follow this procedure ( which I cant remember lol. ) both motors will go through a full rotation breaking the stop pin that tells the motor to stop.
Hope this helps. Good luck
Jeep wj 2003 2.7 crd. Rough country 4inch long arm lift. Tom woods front shaft. Custom fab Rear tire carrier. Polish fender flares. Gas tank lift. 305x70x16 cooper stt on 16x8 black modular rims.