The cover is a water resistant product and not waterproof as stated in the FAQ and Features pages on our website.
Leaking will occur along the rail where the panel seals intersect the inboard rail seal. It is impossible to get those two seals to mesh closely enough to prevent water from dripping past that point. The water then may travel underneath the panel, along the panel seal until it drips off from what appears to be the center of the panel. Water tension can even permit water to run slightly uphill. We're not saying this is happening in your case, just that it might be.
Pictures are worth a thousand words and we would be happy to take a look at your cover. Please view the photos below and send the same shots of the cover on your truck to support@peragon.com. This will allow us to look over the install and view the seals on your cover to see what can be done to minimize the leaking you are experiencing.