I have the same issue. I found this fix on another ford forum site. I don't know if it works. I still have to try it. If you try it first, let me know....
"Although this is an older post, I thought I would respond as I found no answer on the web. If the rear shade goes up part way and stops, and if you cycle it again, it goes down, pops, and then goes full up, the hard stop for the motor is wore. To repair this I removed the assembly (6 bolts and a wire connection) after removing the C-pillars on both sides and the parcel shelf of course. After assembly is removed from vehicle,remove the phillip head screw holding the plastic oblong part that ties the two actuator rods together, and lift it off the motor shaft. File the hard-stop square (it has the two small slots on top of it) and grind or file the motor shaft down about a 1/16" of an inch keeping it flat and cool (this will give more surface area to contact the hard-stop). Reassemble with the shade in the full down position, make sure the oblong part is installed so it is close to the hard stop. Reinstall the screw, reinstall the shade assembly and test. Now when the shade is retracted the oblong part turns until it hits the hard-stop, the motor reaches a peak current and turns off, when activated again, it turns the opposite direction until shade is fully extended and again uses the over current feature to turn it off. The popping noise originally heard is simply the oblong part riding up and over the hard-stop rather than it solidly stopping it."
