I've got a Pro Top removable hard top that leaks BADLY. I stopped a few smaller leaks but the rain pours in by the back hatch. I ordered a new trim piece that seals the hatch to the door but something is wrong. It looks like the rear hatch is warped, but I'm not sure. If I put a straight edge along the bottom edge (below the glass) it seems to be 1/4" lower in the middle. The door (with the seal trim on ) drags so hard on the hatch there that it will tear off the rubber wipers on the trim ( that is what happened to the old one). Could someone check their top and see if it is also lower in the middle or not. At least then I'll know if I'm on the right track. I may be able to use a heat gun to gently flatten the warp but don't want to risk doing it if that's not it.
Thanks

Spoke to the people who made Pro Top hardtops and my hatch must be warping /sagging. It is polyethylene and may flow back if I heat it with a heat gun. If not I may have to cut it and plastic weld it back together

Let us know how it works out.  There was another post in here from a hard-top owner that found that the top was bent out of shape due to it's storage during the summer.   I believe he built a jig to help bend it back into shape so it fit properly, then stored it in the jig during the summer.

I forced a wooden shim between the hatch and the top of the tail gate and worked my way across the hatch with a heat gun. I could hear it relieving the stress as I heated. It moved the plastic up enough to clear the seal on the tailgate. Kind of surprised at how easily this top softens with heat. Don't see how it would last in any really hot area. Now that I know how easy it is I think I'll try the front piece; When I looked close ,it has also drooped down on the edges a bit and the door rubber hits it and causes wind noise on the hwy.

ive got the same problem with mine. i went through the car wash the other day and water poured down the back hatch. if i were you you should have bought a fiberglass top.

It came with the truck. I also have a Sunrunner with a fiberglass top (Best Top I think) and even though it doesn't leak, it rattles like crazy. The Protop is a lot quieter but a pain to get watertight. Now that the back hatch is better I notice the side windows leak a bit. I just bought a roll of the rubber seal and will change it out.
One of the mechanics at work said that, at the dealers, they used to "refresh"  hollow seals by inserting the gray foam strip that is used to fill cracks in concrete into the hollow center. I tried it with the seal around the back hardtop  and the seal on the bottom of the hatch and it did help.

What year truck?

92 Tracker and 92 Sunrunner.

Finally stopped the water! I had to heat the bottom of the hatch again, pushing it up with a piece of wood until it was straight across. This gave me enough clearance to install the plastic tail gate seal I got from Accessories4less.
I tried to find the same 2 part locking rubber seal that came with the top but no luck. I did find one that was REAL close at a local glass shop ($30 for 12', enough for both quarter windows)
AS-1179, 1/8 x 1/4 two part weatherstrip. It is a little thicker in the middle and makes it really tough to put the window in. So I used the glass to make a plywood template 5/8" bigger ( the min.clearance) and checked if that went in the opening. I found that the opening wasn't the right shape. Whoever cut the original opening went by the "close enough "method. When I straightened and trued the edges of the opening with a small grinder I had to take off less than 1/8" on two sides to fit the template in. Used the install tool and soapy water to install glass.  Butyl caulk sealed the joins and a little under the edge. NO water from the last few storms. I won't try a car wash as, with my eye near the strut, I think I can see light coming in from the front top corners. If I shot a hose in that spot I'm sure it would leak. That will have to wait until a really warm day.

Now after all that work is the first hot day going to warp and bend that top
ruining all your work? you might think about some white roof sealer or something
to reflect the heat if the top is black like the others I have seen

Wild

Got an update on my removable hardtop. I started in months ago trying to stop the flood in my Tracker. A few times I thought I had it beat but still ended up with water inside. I had taken the body off and repaired the many rust spots in the floors and now I know why they were so bad.
Water channeled in at the seal between the hatch and the tailgate(got a new seal & straightened the hatch with a heat gun) ,leaked in at the windows (new rubber), and blew in at the top corners of the roof. The shape of the top follows the outer shape of the metal roof section but NOT the shape of the piece with the seal rubber on it. This left two spots of about 1/2 " x 3 " in the corners where wind forced water in. Tried closed cell rubber to plug the holes but still had water. Here is when I lost my patience and siliconed the top into place. Completely lost it when water still showed up on the back deck. The top HAD two pipes as roof racks. They were just pushed into holes drilled in the plastic. Not a chance that they wouldn't leak, can't believe this is the way they were made. The water ran on the inner roof headliner and came out in different spots at different times. Some of the water I blamed on the other problems must have come from theses holes. I tried sealing the pipes but it only lasted a few weeks.
I had a local guy plastic weld the holes shut,the roof rack wasn't good for anything anyways.
The only reason I didn't just get rid of the top long ago was that I was so pissed of at it I was going to make it work. I looked at a few others and they all were the same. Heads up if you have one. 

Well, THAT would explain why the guy that needed the new soft top GAVE me his hardtop  ... Stupid thing doesn't fit right for nothing.    Looks like one of my dogs is getting a new house.