I guess I'm used to jeep doors being more utilitarian than most other vehicles. I know there are a number of fixes for the same issue with hardtops, but not the soft.
Is this a 2 or 4 door? When you say track, do you mean the door surrounds or the dip in the material above you? If you are getting a lot of water on the door surround, your seal at the front of it possibly failing. They are simple foam pads, at least on the four door. I can't really speak to the 2 door, though it should be very similar.