Several things. First, inconsistencies in ogive construction. Your calipers and your die are likely using two different points on the bullet to measure from.
First rule out your measuring device. Does it it consistently read the same thing each time on a the same round?
Next look at the press and caseholder. Is it clean and linkages lubed? Are you using the same cam over pressure on the handle each time? Using a different "technique" on the press handle can account for a few thousandths, maybe not fifteen thousandths like your are seeing but tolerances can accumulate.
How consistent is your neck tension, and is this a compressed load?
Finally, look at the bullets on the finished rounds you had trouble with...are you seeing a bright ring where the seating stem cone in the die contacts the bullet? If so, the micro, perhaps not even visible tool marks left from the machining of the die stem can act like a fingerprint and give the stem the ability to hold onto the bullet, causing the bullet to move some on the upstroke. If it is severe enough sometimes you can even hear a little popping sound as the stem "lets go" of the bullet, or you may feel this through the press. To fix this take the die apart, get some 000 or 0000 steel wool, sacrifice a .22cal bore brush by chucking it in a drill and as you spin it let it pick up some of the steel wool. Form it into a cone shape, and polish the inside of the seating stem. Slicking up the seating stem will improve this problem more than anything.
Even so, if you want seating depths that are within .001 across all the rounds you will have to intentionally set the micrometer die to a setting you know will be a few thousandths long, seat a round, measure it with the comparator, then adjust the die the number of thousandths that specific round requires to get the exact depth you want. Reset your die to the long setting, and repeat this process for each round.
