If the cartridges chamber easily it cannot be shoulder bump related. Must be something to do with case body dimensions. If the rifle is not a serious competition rifle and they chamber OK and shoot groups like the other cases, I would not worry about it. Can you measure a difference in case body diameters at several locations. Never used a case guage in fifty years just load and shoot. The more things you measure the more problems you think of. Both my rifles shoot under .400" with simple reloading methods.I have a small puzzle with my reloading brass. I have about 120 2x fired Lapua 6 br brass and I check the cases with a Wilson case gauge. I resize with a full length Wilson die and most of the brass is fine and fits the case gauge perfectly.
However, I have about 8 or 9 cases that seem a bit odd. The case head sticks out a bit more from the case gauge than the others. Not a lot, and it might make no difference in the gun but it still is odd. I bumped the shoulders about 0.003 like all the other cases and I was unsure about these 8 pieces so I reran them through the sizing die and as far as I can measure, it seems the shoulder was bumped back the same as the rest of the 120 and I trimmed the brass to virtually identical lengths. Yet these 8 behave as if the shoulders weren't bumped back far enough. What is going on? Should I just bump the shoulders back a bit more so that the cases fit the gauge as perfectly as the others?