Perhaps I'm misunderstanding your use here so bear with me a bit. This is based on using mine together with the bullet & chamber comparator.
I thought the way to set up the gauge & calipers was to attach the adapter to the jaw that moves, using the offset cut either centered for measuring cartridge OAL ( so the tip of the bullet can be measured on the knife edge of the fixed jaw) or offset for measuring the case from base to datum line where the case base is measured off center to reduce primer issues (more later on that)
. Then the caliper is closed to lightly grip the adapter, the locking knob tightened & the caliper set to zero. This is supposed to eliminate play in the fit of the adapter to the caliper blade, & between the adapter & the caliber specific gauge by applying a little compression when tightening the set screw for the caliber specific gauge & the thumb nut for the adapter.
To use after this you were supposed to measure the round, take a note of the reading which would be fired case length from base to datum line & use that for calculations.
I'm just wondering if trying to use the caliper as a zero measure for the "standard" case to allow a +/- tolerance or deviation, instead of zero with the adapter is causing an issue?
One other thing I discovered that made a difference was the fired primer!!!! Sometimes there will be distortions to the cup in firing that cause false reads, you might want to decap a short, long & "normal" case & remeasure, just to eliminate that as a possible error source.
Sorry if I misunderstood your zero setting, it was a bit unclear to this foggy ol brain.