William,
I think that you are having a nominal update problem. DNSC has had many discussions on this situation. I would recommend that you measure the points for the primary plane, secondary and tertiary and create your coordinate system. After which you re-construct the plane to measure the wall thickness from. By re-constructing the plane in the new CS the evaluation should be correct. If you are using a large probe, the planes are on angles from the probe, etc. I would recommend that you re-measure the points to keep any cosine error from occurring.
Ray Admire
Lead Quality Engineer, CMM Programming
Lockheed Martin Missiles and Fire Control - Dallas
972-603-2074