part not square to coordinate system

[[Be...]]

We have a part that has very few planes that can be aligned to.  What is worse is that to fit it in the cmm and measure things it needs to be NOT square to the cmm.  After a few hours, I am still working on the alignment process.  Without too much detail,I have found that the software is not putting points where i click them!  I think that if I can solve the problem if I can figure this out.

I have a plane that is NOT square to the coordinate system.  I need to place a point on that plane.  I click on the model and the point ends up not on the model and not in the location I clicked.  The point ends up around 0.03" off to the side and about 0.01" above the model by eyeball estimation.

I have tried adjusting the view and this does not fix the problem.  I really don't understand how it is picking that location.  It forces the ijk of the point to be square to the coordinate system.  I can manually fix that even though it fights me.  

Is there a thread for people who have fought this kind of thing before?  I came from using Verisurf, Polyworks, and PCDMIS.  None of them had issues with handling parts that were not square to the coordinate system or did not have nice tidy squarish features to work with.  Why is Calypso so bad at this?