[Unclenick]

Double-check for measuring errors. Try rotating the cases 1/3 turn and measuring again. If the lock up has any flex, the face of the caseheads might not be 90° to the case body axis. Same can be caused by a chamber not coaxial with the bore. Not entirely uncommon, unfortunately, though my own Encore chambers look pretty true.

Watch how the case head meets the moving caliper jaw. The offset in the insert adapter in that gauge is necessary for using it with their Overall Length Gauge, but can trick the user into angling the case head against the moving jaw of the caliper.

Try backing the body die out a little and running the short cases in. Do they grow longer now? If so, you just need a different setting with them to get the shoulder where you want it.

When a primer fires it can drive a case forward enough to change its headspace a bit, but I don't recall getting as much difference as you're seeing, which is why I wondered if the caliper technique might be a factor. I see two thousandths difference pretty routinely.

Try skipping the body die and just use the collet die a couple or three load cycles. Do the cases get closer in shape? Unless something is producing of off-90° effect I mentioned already, that should tighten them all near the upper limit.