There is definitely flexing occurring or the cracks wouldn't be there. Since it is happening at the corner of where the non-flexing camper sits, it seems obvious that is causing the crack. Fill in the two valleys at the edge of the camper tub (inboard of where to two bed seams are) and put one sheet of pink Styrofoam insulation in the truck bed to let things flex better and you should be fine, once the repair has been made. I hadn't noticed where the crack occurred in relation to where the camper sets until after my first post on this subject. It is an easy fix, and my bet is it won't happen again if you do the above listed mods.
Also, I always put camper guides and a front camper stop on all my truck beds that are going to carry a camper. Remember, "shift happens". LOL
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Good luck and happy camping.