Interesting, I'd love to hook our pressure gear up and have good look at those two barrels. There has to be some major differences in chamber or bore. Have you slugged the barrel? That will often show up constrictions and other bore variations. Bring them down some time if you would like to, and we'll stick strain gauges on them and check them out.
Anyway, this is the exception that proves the rule, and doesn't mean a reliable chronograph isn't your best tool for general load development working up to loading manual maximums. I have well and truly qualified this in the post above.
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