How to fix your leak
I put a thule rack on the top and from about 4 years of a case, gas, and I am sure up to 250 lbs up there it started to leak. What I had a difficult time was understanding where it was leaking from was not where it was leaking inside. The leak was traveling down the roof support leaking all the way to the front. The fix was to carefully remove the screws that held the rack on the roof, clean all silicone off and reapply. I put a generous inside each hole and around the head of the screws and put it back down. It took about 3 hours to do the whole line of screws from the very front to the back. The leak stopped no problem. What would happen is water would travel along the track like a gutter and find the hole. It would only leak when sitting, makes sense because when driving the water would not travel along the rail like a gutter.