leaking topper

Just got a 95 bronco and it has started raining hard here in Portland, topper has a leak that I can't seem to track down. Water is pooling up on inside of windows of the topper under the window seals, water is finding it's way in not through the window seals themselves? Well not up and under I dont think? It gathers around the trim under the window seals and drips in. I used some silicone caulk on the out side of window trim, but still getting water. Any ideas?

Thanks