Theres really no avoiding that, the water that runs down in the seam is going to stay there until it dries. Best thing to do is to not roll your window down for at least the first few hours after washing.
Leave the windows up immediately after the wash and park in direct sunlight if you can... the heat will at least dry it out a little faster. On a summer day if I wash, then do the interior (vacuum, clean, dress) out in the sun the water is all but dried completely. In winter it takes longer.
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