Any difference in the dimensions of the primed brass and the loaded shell?
Is the primed brass full length resized or just primed right out of the box? If they are just primed and nothing else, the shoulder could be a bit farther forward thus headspacing off the shoulder and the resized/loaded shell is headspacing off the rim which is allowing the shell to enter a little further into the chamber.
This is probably not so since your guages tell us the headspace is OK but that's all I can think of.