Uneven annealing causes really bad runout too. Did you anneal the cases? Even heating is critical.
Another idea is to raise the expander ball upward and close to the neck area of the sizing die as possible. The higher the expander ball, the more support the sizing die gives the case during expanding.
Hard case necks require a lot of tension to pull the case over the expander ball, which can cause or contribute to runout (stretching too). If you hear a sound like "Squawk!" when pulling a case over the expander ball, either the brass is too hard, or the inside of the neck improperly lubricated, or both. If yours pull hard, anneal them, then lubricate inside the necks with powdered graphite.
