smart window

I had to replace the door on my 15 R/T. After I replaced it the window stopped coming down 1/4 inch when you open and close the door. Both windows roll up and down on auto, passenger side goes up and down 1/4 inch when you open and close but the driver side does not. I used ALL of the same parts...

I have a 2012 Challenger and when I open the door the window will do the 1/3 drop but when I close the door it will not automatically close again. I have to click the button to roll the window fully up. I have tried to run the Calibration steps but no luck.. Have you seen this and if so what...