Today I pulled one register and the boot/box is flush to the drywall. I also put the thermometer up into the duct, well past the boot. Same result, still gaining about 5 degrees. So the boot is not the main source of infiltration. I also went over to the other neighbors' home who's house is exactly like mine, and who had her ducts re-fastened as well, and she has the same anomaly going on, gaining about 5 degrees between the AHU supply and the register of the shortest duct run.
Its not a mystery. You are picking up heat from the attic. Cool the attic down. Add a attic fan.