I don't have any doubt that your truck will haul that 5th wheel with authority. If you're exceeding any of the capacity ratings associated with your truck, though, you may be stressing the frame (and attached body/bed panels) beyond what it was engineered to handle. As an example, when calculating your payload, you are to include passengers and cargo, and cargo includes tongue/king pin weight. You stated your payload rating is 1860 lbs and your pin weight is 1660 lbs. That would leave only 200 lbs for driver/passengers and anything else you throw in your truck. That alone has potential to be the cause of your tweaked truck bed panel. And we haven't even addressed what you're packing in the 5th wheel and how much you may be exceeding your truck's GCWR.
You might indeed have a defective bed panel. If I were in your shoes, though, I'd trade that truck in for an HD model ASAP. Best of luck on this issue and future travels, regardless!