After further inspection, I see where the main problems were on this cover. I wish I took pics before I filled up the areas with black window silicone, but anyways upon further inspection I could see a large gap where the drain spout is cut out and attached to the rail.
Apparently these things are made to order and Bak does not have decent quality control, there was a large 1/2 inch gap in above mentioned area on both sides so say you were in a heavy rain storm or your Titan is parked outside, when the water runs down the rails toward the spout area if it is constant it will overflow and leak into the bed. This was fixed with a generous amount of black silicone. I also siliconed the rear of the rails at the tailgate because they just drain into the bed as well.
The gaps I mentioned on my previous post were at first filled with weather stripping and because of the cheap tape, it failed. These areas were also hit with the silicone and now there are no leaks what so ever.
Im not sure if anyone else has leaking from their Bakflip, is so I recommend you take a look at the areas I described and see if the drain is poorly cut or you have the gaps near the cabin. They are quick fixes, but you would expect these things to be taken care of when made at the factory. Its still a great hard folding cover! Im considering finding new clamps for it as well, since the ones given to you barely grab the metal if you have the plastic trim going around the Titan. Hope I helped with anyones leaking problem.