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When I looked at the picture it appeared that the water went over the glass and then down the inside and then wicked (capillary action) down the seal.
I believe when the cars were shipped there was a coating on the seal something like wax. It left a residue on the window so people removed it from the seal to keep the window edge cleaner. It was water resistant and stopped the wicking from happening.
You could experiment with some kind of a water resistant coating to determine if this is the cause. [Chapstick would work or a silicone spray or grease to test.]
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