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My glass targa top has been leaking for a few months now right up near the front corners of the top. It never leaked bad just more of an annoyance when it rained. The water didn't appear to be leaking around the seals and windows but rather coming through the seams on the inside of the top where the top was put together. After a lot of examination, trial and error, and head scratching I finally found the problem. The problem was with the seals on the outside top edge where they meet the top. It was completely unnoticeable until I actually started pulling on one side's seal to see how hard it would be to remove it. The sections of the seal where I normally grab the top for removal would pull away from the top. The back portions of the seals on each side would not easily pull away from the top. I used a large (fairly blunt) flat tip screwdriver to reseat the sections of the seals that were loose on each side and problem fixed!!!
The problem is that there was no way to tell that the seals weren't fully seated on each side of the top until I just started pulling at them. Even then I wasn't convinced that was the problem until I squirted a little water in the looser area and it came out on the inside of the top where my leaks had always been. Since I live in Atlanta and it rains here every day now, I have already had several opportunities to test it out.
I've searched pretty thoroughly through the archives and have not seen this fix but figured if it happened to mine it has happened to others. I read a lot of posts where glass tops were replaced under warranty for leaking; I wonder how many of them had this same problem.