Depends on the lube you use but for bigger calibers (mostly .358 and up which have a lot of bullet/brass contact relative to smaller calibers) I intentionally leave both one shot and graphite lube on the inside of the necks. Otherwise with virgin and even once fired brass I get crazy runout due to bullet seating friction, even at low neck tensions and with perfect chamfers. I've shot these lubed-neck rounds vs unlubed neck rounds and even at 750 yards they shoot into the same group.
Point being: you can leave certain lubes on the inside of your necks: all the graphite lubes and also one shot.
Though it sounds like you've already solved the problem.
