Gary,
This may sound odd but check to see that your X,Y & Z axes are counting in the right direction.
X=positive to the right
Y=positive to the rear
Z=positive up
You mentioned that YOU upgraded the software to PC-DMIS. Did you do the upgrade or did B&S do it. If they did, this should have been checked and set after the install. If you find that one of the axes is counting backwards, it can be changed in the CMM setup menu.
Mike
Call me at 636-519-0699 if you want!