Leak from the unknown
First check the "reveal" of the windows. Go to the driver's side and compare to the passenger's side from the outside of the car. Do you see any differences? (A millimeter difference could be your issue.)
Second, check the rear guide inside the door. The rear guide slides up and down a track mounted to the back of the door. Peel the plastic back and make sure the guide is still firmly attached to the metal bracket attached to the glass. Sometimes, these guides break off and cause problems.
If your reveal is off and the rear guide is in good shape, you should be able to adjust the rear window stop to allow the glass to extend farther and seal better. There is a front stop and a rear stop inside the top of the door. They are made of white plastic and sit inside the door panel. You just loosen their screw on the door panel to move them up/down.


