Mine was the same way.
I just had mine completely redone on the inside and the guys doing it were supposed to have sealed all the leaks. Guess what they didn't. You need to caulk around each post of the rail, the cleats, your light base(if you still have one), the navigation lights, the horn, around the access hatches. There was also some talk about the tha area where the lid and the hull are attached (Rub Rail) not having a good bond. Might want to caulk around that area also if your still getting wet on the inside.