Originally Posted by sharper4
Most of the water seems to be coming in from this general hinge.
At the bottom edge of your photo, it looks like the gasket on the BakFlip rail is not sealing against the plastic cap on top of the side of the box.
I had that problem when the BakFlip dealer first installed mine. Rather than mess around with the dealer, I removed the cover and rails and used DAP gutter seal to reinstall the BakFlip rails.
They don't leak anymore, but if you hit the BakFlip with a water jet, you can overflow the rail gutters that drain to the tubes by the cab. Also, if you use an air blast (like a leaf blower) to dry the BakFlip after washing, water trapped in the folding gasket seam can overflow those same rail gutters.
It took me a couple of tries to get it lined up right, but I'm very happy with it now.
I hope that helps.