Are you sure the cover is leaking? Let me explain that...
On my hard cover, the water gets trapped in the mounting rails, but instead of going out the front drain holes it flows back and out the end by the tailgate, and into the bed. My issue is the mounting rails not draining properly and had I not seen it happen by opening the tailgate and seeing water flowing out the rails, I would have though it was from the rear seal, but in my case, it isn't.
Water flows into and out of the lower channel in this image, it hits the tailgate and instead of all of it flowing down and out, a good portion makes it back into the bed. This is on an extang xceed.