If you are measuring from the case base to the bullet tip, and you are seeing variations in overall length by a few thousandths, it could be due to a few thousandths of variation in bullet length, or in diameter of the ogive where the seating stem contacts it, or both.
To check for movement of the die parts. once you have the desired adjustment set, make a witness mark, or use a torque-seal type product (or nail polish, or model paint) a drop where the stem and lock nut meet, and perhaps a second drop on the lock nut and die body contact. Choose an easily seen color. Let it dry completely, then do some more loading. If the parts move in relation to each other, the paint will crack.
Consider measuring some of your bullets for length. Small variations are normal. Check to see if the range of variation in the bullet length is consistent with the variations you are seeing with your loaded rounds. IF so, the most likely explanation is that the bullets simply are slightly different lengths and the seating stem is contacting them consistently and what you are seeing is the difference in length between where the seating stem contacts the bullet and the bullet tip.
