Alignments using Cylinders

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I have a part that uses a plane as Datum A, a cylinder as Datum B, and a plane as Datum C. B and C are perpendicular to A.  There are other cylindrical features(ie OD threads) that are concentric to datum B.  I believe that there is projection error being introduced using a cylinder as the secondary datum that makes calypso report that the features are out of tolerance for position.  I check the part using other measurement techniques and it says its good. 

Does anyone have any tips or suggestions to dealing with potential projection error that gets introduced using 3D features(Cylinder) as a datum? 

What is the recommended way for building these types of datum structures in Calypso to insure that the machine reports accurate results?

Thank You!