Question was raised above as to how much of the neck is sized. Not all neck sizing dies with bushings will size the entire neck down to the shoulder. Redding, for example, will not.
Also- how are you measuring the run out? With what tools and how are you doing it? It might be the tool and it might be you.
Also- how are you measuring the run out? With what tools and how are you doing it? It might be the tool and it might be you.