Unless all your initial loads were fairly hot, you can expect considerable variation in base-to-shoulder measurement. Run loads through all those cases again, preferably all hotter loads, sizing necks only, then measure them again.
Did you happen to measure the shoulders of any virgin cases? Keep in mind it's not unusual for them to have on the order of .008" headspace (in mass-produced chambers anyway - yours may well be tighter.) so there's a considerable range they can settle within after one firing if the loads range from mild to hot. The softness and consistency of the brass has a bearing on this as well.
If you are not sure about your measurement tool / technique, just record the measurements for 5 or 10 cases chosen at random, then go back and measure them again, see if you duplicate all the original values.
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I did not measure the virgin cases. In hindsight I should have.
FWIW, I neck sized all the cases and left the shoulder alone. I'll revisit the measurement again after they are fired.