I have been using CMM Manager for 14 years....  and I have been doing my alignments in this order:

Level ----  Origin -----  Align (without setting to origin)  then I would sync CAD

Today I have had some time, and so I was surfing around on the Community board, looking at posts trying to learn some helpful hints and saw that the "Proper" sequence is:

Level ---- Align ----- then Origin..... 

Does this difference in method mean that I am getting bad alignments ??