I like to keep things simple and use as few steps as possible. I've had good luck with Redding FL bushing dies pushing my shoulder back .002" and leaving the expander ball in. With good brass like Lapua I get .001" run out. I also have good luck with Redding and forster competition seating dies. One seats bullets as good as the other. .001"-.002" run out. I believe too many steps forming brass is can add up to problems like you're having. I use the same Sinclair run out checker you have and if not set up correctly it can give some false readings.
Hope you get your problem worked out.
Billy
Hope you get your problem worked out.
Billy
