Mine leaks across the top as well. I sealed my lights, which were leaking around the bolts and now that is fine. But the top seal against the window frame is not tight. It was full of dirt and bug shit so I cleaned everything and went for a test ride in the rain with the roof liner removed. Still leaks across the top of the windshield.
I'm thinking a small 1" wide piece of rubber the length of the window, jammed under the orange roof and it's frame, then it would lay across the top of the windshield and deflect water away from that edge. Water just lays in there and you are right it is not compressing the rubber seal tight enough to do the job.
If the orange roof had extended another 1/2" this problem would be virtually eliminated.
Let me know if any finds another possible solution.
Thanks
Brian