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Straightness of a Shaft (GD&T)

So I have a shaft with several different diameters that is always bent between .010 and .020 off the CNC machine. Our internal print calls out for a bunch of true positions. I told engineering to change it to straightness because that seemed more intuitive (since the part is always bent so much). Now I am writing the CMM program for it. I probe each diameter, create a 3D line between them, and dimension straightness of that 3D line. I'm only getting a result of .001, but when spin the part on the optical comparator it is for sure .010 bent...Any ideas what's going on here?

I just need a consistent way to measure the average straightness of the part that can be validated with a dial indicator or optical comparator.