could be that your seating die contacts the bullet in a different location than your measurement tool. If the bullets have just a little variation (which is very possible), this could lead to the .002" variance. May just be the bullets and not your equipment.
One other thing that may help, after you seat the bullet, rotate the cartridge in the shell holder about 1/3 of a turn and seat the bullet again, then rotate another 1/3 of a turn and re seat a 3rd time. This seems to reduce some of the variance in my seating depth.
Hope this makes sense.
Good Luck