Bullet seating depth can be affected by the the manner in which the seating plug engages the bullet. Jacketed bullets are very uniform which results in very consistent COL after seating. Lead bullets can be less precise and may engage the bullet seating plug less uniformly which can lead to variations in COL after seating. So you can't assume that the bullet is seated to the same COL every time.
One thing that may correct or improve the situation, if you haven't already done so, would be to reduce the case flare to the absolute minimum to prevent lead shaving. This would tighten the friction fit of the bullet further and hopefully correct the problem.
