OK, heres an overdue update...I do use a VLD chamfering tool so that was not the issue.
I went back and started at the beginning with some recently fired Lapua cases. With these I checked runout after every step in the process and found they had very little to none after they were fully prepped. When I seated a bullet in these cases I was back to my old, good, low runout numbers.
The only thing I changed was that the press and all dies involved got an extremely thorough cleanup. I did find some buildup under the universal shellholder base plate which could have forced the case to sit off square with the rest of the press.
I thought I had these things covered before but apparently this was more a case of "garbage in, garbage out" than any big mystery. I sure wish I had had the good sense to check the easy things first before I got into all the checking, measuring, and general hair pulling I went through.
Thanks to those who had some input on this. If something good came from it, at least I have been through my loading process pretty throughly now and looked at everything pretty closely for problems or potential problems.
"My greatest fear is that after my demise my wife will sell my guns for the price I told her I paid for them"
-don't know where it came from...but true