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Concentricity Changes a lot when I rotate a part 180 degrees.

I have two cylinders on a part that need to be concentric within .002". I noticed that on some parts, not all, the concentricity reports out of tolerance at .0039 for example but then when I rotate the part 180 degrees, the concentricity is suddenly .002 or less.

I align the part by measuring a top plane, leveling to this and setting z origin. Then I measure a circle with 9 hits and make this the x and y origin. Im not locking rotation as I really dont think it matters in this case since its a circular part anyway. I then measure the datum as a 3 level cylinder with 9 hits each level, then measure the next cylinder 9 hits 3 levels.

I don't see how rotating it 180 degrees changes anything especially since I'm taking 9 hits at each level on diameters less than 2.5 inches I should be, in my mind, hitting enough spots to capture anything weird going on with the part. What am I doing wrong here? Thanks.