sorry to hear about your repairs on the truck.

just a FYI...panel bond isn't designed to be used on anything except the factory joining locations between 2 panels. or otherwise know as the factory lap joints, like where the 1/4 panel meets the outer wheelhouse in the wheel opening moldings screw into. of the pinch weld flanges under the glass bonds to or where weatherstrip goes over in the jambs.
it's not designed to be used in the middle of a flat panel near a body line where a lot of people sectioning a lower panel to a upper panel. you will have the same problem like using fiberglass to fill seam joints instead of body solder on older cars. there will be expansion differences and the seam will show up when it warms up. i have seen a LOT of shops use it that way and have the problems you describe later on.
it also doesn't like to have body filler spread over it. this will lead to adhesion problems and rust forming under the paint like you describe. if you HAVE to use it that way, CLEAN the lap join as best as possible to remove as much adhesive as you can. after that spray a couple of coats of epoxy primer down to seal off the area and then scuff up the epoxy and spread filler over the epoxy. you will still have expansion problems but there won't be any adhesion problems.