Once a bullet seating stem's set and locked, there should be no difference in OAL regardless of how the fired case was sized. This assumes there's no interference between either case and the seater die body's dimensions.
My guess is the seating die wasn't screwed all the way down. If it was and you just screwed the seating stem down on your test round and stopped when the least contact was made, that might have caused the difference.
Last edited by Bart B.; November 17, 2012 at 08:01 PM.