I'm not sure of your exact problem, but the one time I had problems with my auto up control on my Civic was when I accidentally caught the bottom edge of the vent in the window track. I'll try to explain. The bottom edge of the front window vent is made so that just the corner closest to the vehicle in engaged in the window track. So, the bottom edge of the vent should "stick out" from the window at an angle, with the closest edge in the track, and the outside edge angling away from the vehicle. If you force the entire bottom edge of the vent into the track, it will "spring load" the vent, and cause too little clearance for the window. Don't know if that helps or not. If you can't solve it, please contact the supplier. For the price you paid, they should work well when installed accordin to instructions, so go after them to tell you how to do it, or get a refund!
Bill