Note that the
length of the cylinders will be different,
and has an effect on the perpendicularity result. An auto cylinder gets the length from the CAD Surface, while the constructed (or measured) cylinder gets its length from the hits (ie. shorter than the auto cylinder). You can test by adding "projected zone" - (P) <length> - to your two perp dimensions to verify that they give the same result when applied to the same length (assuming the hits are the same).
What version of PC-DMIS? I believe the length calculation for auto cylinder has changed during the life of PC-DMIS.