I have an aluminum block that is roughly 3" x 5.5" 

I use 3-2-1 to pick up the part, then on one of the surfaces I use the plane feature to check flatness. I pick up 16 points and it spits out a flatness of .0012"

When I lay the part on that surface on a  surface plate and put an indicator on the other side, I can rock the part around .002 - .003" there is clearly an issue with the flatness reporting with the CMM. I have calibrated the tip multiple times and increased the the plane to 32 points with the same results.