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I have been having this issue or a while. Intermittently when I open the passenger door the window does not drop to clear the seal. The door still opens obviously with some resistance and have to turn car on to drop the window using the button just to get the door to shut.

I know some makes have re-initialization sequences to set the window/motor right. Is there one for the Challenger?
 

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This may help, just a place to start. May work but if usually only if you lose both sides, try it anyway.

Symptom/Vehicle Issue: Customer concerns with improper glass function such as “glass will not go down or up all the way” (Expressup / Expressdown) or “drop glass will drop but not far enough when opening the door” (Smart Drop Glass) are symptomatic of bad calibrations. This should not be confused with complete loss of calibration and the distinction needs be clearly understood for proper diagnosis. The repairs are quite different.
Diagnosis:
Bad calibration, the Expressup / Expressdown works, but only somewhat. Loss of calibration examples are “expressup does not work at all, glass moves ½ inch and stops and you need to lift and hold the button to raise the glass fully” (Expressup / Expressdown), Or, “drop glass will not drop at all when opening the door” (Smart Drop Glass).
Repair Procedure:
1. Bad calibration conditions: it is vital to first denormalize the door control module ECU, then recalibrate with the engine running. Trying to relearn the calibration alone will not work.
2. Loss of Calibration : On the other hand, for complete loss of calibration, denormalizing is not required. Only the relearning process is required, again with engine running.
3. CLEAR/DENORMALIZE :
1. Check and repair any door module Diagnostic Trouble Code (DTC)(s) before proceeding.
2. Using a scan tool, under the miscellaneous functions menu select (Denormalize Window/Reset ECU), and follow the directions to clear/denormalize the door module memory.
4. RELEARN/NORMALIZE :
NOTE: The battery must be fully charged or the vehicle running before proceeding.
1. If needed, place the vehicle battery on charge or have the engine running.
2. To relearn/normalize the door module, start by raising the door glass to the full-up position by pulling up on the window switch to its second detent and hold the switch until the door glass is fully closed. Continue to hold the window switch up for two seconds after the door glass is full closed.
3. Lower the door glass to the full-down position by pushing down (depress) the window switch to its second detent and hold the switch until the door glass is fully open. Continue to hold the window switch down for two seconds after the door glass is fully open.
4. Check the operation of the express-up and express-down features.

Good Luck!
 
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