The rubber piece (see circled) could be getting in the way of the window channel strip from popping into the window frame sheet metal. If you try popping your door panel and open it a little from the top, it will hopefully become clearer to you. Suggest using a trim removal tool or a flat head screw driver and gently insert and open the top sides of the door panel. You will have to remove the inside door latch cover and possibly the bottom cubby screws.