I'll say from the beginning that this problem could be related to my OEM rack, but I just wanted to get others' input. When it's cold, meaning lower than 40 F, outside, when I open my driver door, the window doesn't always lower enough automatically. When I close the door, it hits the roof trim and doesn't seal properly, leaving about 1/8 to 1/4 inch gap where it catches on the roof trim. This happens about 10% of the time when the temp is hovering around 40 degrees, but more often when it's cold.
I say it may be roof related because it's known that when the oem roof rack is installed, it forces the trim down a little bit, but if that's the case, why does it only happen when it's cold.
Anyone else seen this?

 

I have an OEM rack as well, but mine does not push the trim down. I do know that if you don't have the rack fully into the roof then it will displace the trim. Might want to double check your rack to see it is mounted properly and that the distance between the "feet" of the rack is correct, as if it is too wide it may cause the problem you are experiencing.

Hope this helps.