And this is why I use Manson Reamers headspace gauges for everything now. PTG is a major PITA to deal with in my experience.

If the gauges are visibly sitting differently in the chamber (especially on two different barrels) then obviously there's something going on. I wouldn't go any further with that project until you can confirm what the problem is. Maybe try using the Go-Gage to set initial headspace, apply 2 pieces of scotch tape to the case head, and then see what the result is? You could also try re-sized cases just to see how they fit in the chamber.