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Government and Boss wants answers

 Haven't posted since I have become a member, mainly because I always seem to find my answer on older post. All except this one. My cmm wont give me a correct measurement. Its a poor musician who blames his instrument, I know, but follow me here. When I manually mike the distance, I get 13.38mm, which is out of tol. however when I run the part on the cmm, It measures 13.325, which is in tol. The Gov rejected 3 of our last 4 shipments because of this. The part is 99.9% dimensioned with profiles. Not all of the 100+dims are measureing this way, only about 7 of them. However, it is the same 7 dims involved with all the 3 shipments.

I also have a question on stacking profile tolerances, how does that work? Please find attached the section of print in question. Wish I could upload the rest but its gov stuff. Can anyone please help me? dont know how the posted pic got way up there but its the best i can do. can anyone help?