I also took a case that was fired in my 30-06, and tried to chamber it. It didn't chamber at all. Ran it through the die with the expander ball removed and chambered again. Again it chambered with zero resistance. So it seems like at this point we can firmly rule out a headspace problem? I will try lubing the inside case neck with some rcbs lube I still have left, and see what happens when I neck it up again.
Now might be the time to measure your expander ball and see if it's a bit over size. You have looked at about everything else. Great thread. It looks like you have it figured out.
kwg