Measuring end mills with a "caliper" is not exactly very accurate. Even a micrometer is not all that good.
Some food for thought: It does not matter what the end mill measures across the flutes. What matters is how wide it cuts. When I really, REALLY need to cut accurately what I do is measure the width of a test piece carefully. Then I cut a slot (on a vector, not going round and round), then chop off the ends and put the two pieces together and measure them.
I also use this technique on the table saw to measure how wide the blade is cutting.
Oh, the point is that using a micrometer or caliper on a large surface is much more accurate than measuring across sharp flutes. Plus, if that end mill is not perfectly concentric measuring the flutes is not telling you much.
"If you see a good fight, get in it." Dr. Vernon Jones