Try giving a case a rub with some emery paper around the base and then some steel wool, just to take like half a thou off the dimension. That way you'll know if its just a die with tight tolerances.
I had a similar problem when chambering Hornady vs Norma brass. Hornady chambered fine, Norma couldn't close the bolt. Gave the Norma cases the above treatment and fixed the problem. The difference was that fine that even the vernier gauge couldn't pick it up.
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