In my opinion the window height needs to be adjusted.
From what you are describing, it seems like the window is dropping too low and going under the rubber seal.
There is a good artical on the pelican website showing the procedure, and the specs for adjustments.
The adjustment is pretty easy, and can be done without removing the door cover.
However, if you don't feel like doing it yourself, you will be able at least to check the adjasment and confirm that is your issu.
I will post a link for you in a bit.
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