Was it a Redding shellholder to match the die? I have seen this once before but in the opposite direction - a FL die from one manufacturer combined with a shellholder from a different manufacturer resulted in cases that wouldn't chamber in any rifle. It didn't matter what was tried in die adjustment, the die was down as far as it would go and any further winding down just meant the press handle didn't go up as far or 'cam over center'. Replacing the shell holder with a different one and adjusting the die meant that the case shoulder was bumped back that little bit more. The cases were milsurp, once fired and I suspect out of a belt fed weapon as they were too long to be chambered in a 7.62 bolt action sporting rifle. I subsequently tried the cases in a matched set of Hornady full length die and shellholder, that worked fine but in keeping with other's reports about the Hornady die the cases were very straight but the force on the press in resizing and then breaking the case out of the die was huge and did not give me any confidence at all! Ended up going back to the original die and a matching brand shellholder, and on measuring there was a noticeable and measurable difference in height between the base of the shellholder where the case sits and the top that the die contacts (the taper in the shellholder to clear the rim of the case and case head was noticeably longer on one shellholder as well).
There's a good chance that something like this has occurred, except that somewhere there is an equivalent smidge of metal missing to the amount of difference you have measured between the two cases (your dummy/once fired and the recently obtained batch). To verify if this is the case, find a shim washer that slips over the .223 case of the right thickness and resize a case, measure it, then take the shim off and reset the die up and remeasure. That will tell you if the issue is the dimensional error (the combo of shellholder and die is missing that amount of material) but it won't tell you which end is missing the material.
In normal operation of a die and shellholder, when setting up for the resizing operation you would set up long and resize down to the point the resized case is just firm in the rifles chamber (unless you are reloading to fit into any rifle in which case you would set for SAMMI maximum case size dimension but 99% of reloaders aren't in this situation). That would usually avoid this situation.
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