That's what I am thinking, I have tried a couple different gear positions with no luck yet. The following pictures show the two gears that are involved, the white gear attaches to the actuator and turns the black gear which has an arm built into it which attaches to the linkage to operate all 3 flaps. The fresh air flap's shaft is attached directly to the black gear. If you look closely, there are two raised gear teeth on the white gear, and one raised black tooth on the black gear. I had to assume that mating the gears up with the black tooth lining up between the two raised white teeth would be correct, but it didn't work. I also now have INPA and SSS software up and running so I can disable any flap memory activation, haven't tried it yet. The noise that this situation generates, the four or five flapping/clicking noises is generated by the white gear turning while the black gear is not, it basically grinds until it can push to the next tooth. Of course the noise is amplified by the duct system.
Anyone who is wondering why I am spending all this time with this, the dealer wants $3000+ to take apart the dash, replace all the gears and actuator, and put it all back together. Car is not under warranty, so that's not going to fly. BTW, I ordered a new set of gears and linkages along with the actuator, $25 from Tisher.