In the hope of helping someone, it may be the window rubbers/seals obstructing the window. The window is programmed to drop if it doesn't seat properly so I recommend running your finger around all of the seals in contact with the window in the door and car body to make sure that it's all pressed in correctly.
For reference I had this after I pulled my door apart to upgrade the speakers. Where I refitted to door trim the rubber seal had protruded slightly and causes friction on the window as it rolled up. I refitted the trim and the problem went away.
Stupidly I managed to do this again after removing the tweeter pod, I put the pod back in incorrectly and again it caused friction on the window. I refitted the pod and no problems.
Now I just don't a$$ about with my door trim...problem solved
