Yes I have tried two different headsets and believe me, the problem is not due to the race not seating. I have the proper heavy race driver tool and a large hammer and I set the forks up securely with a wooden support between the fork blades under the crown. Plenty of force applied to the race. ( I also oiled the fitted surfaces.)
Using the marker pen to monitor metal removal is a good idea. I think I have already improved the situation with the crown race seat cutter. Perhaps I will try it a second time.
And it does appear now that there is no easy way to check that seat for squareness.
Just a final question - if a headset was fully assembled and adjusted on a fork with an out of square crown race seat, what would the symptoms be when turning the forks ? Tight then loose as the forks are spun ?