Neil,
I'm not a pcdmis user. The problem you are having may be because the algorithm is not robust enough to handle the cone construction. Unless things have changed the current routines that CMM's use to calculate partial arcs are not very robust, and unless you have sufficient angle (90?, 120?, 180?, I've heard them all) you won't get repeatable results.
You might try measuring the cone as a surface profile. That will at least tell you if the surface in tolerance or not.
Bob Connors
Lawrence Berkeley National Lab