I think I’m missing a step when programming from CAD before the physical part is available. I don’t have this problem when I do the manual alignment as I go - I.e. before programming the DCC alignment and other features. 

I import the CAD, move the CAD Reference Frame to where I will do my manual alignment (Plane Circle Circle for example) but leave out the manual alignment for now as I don’t have a part to align yet. 

At this point the Refernce Frame is at the home position. 

I program my DCC alignment features and alignments and then do Sync CAD adding it to the program. 

I program all the features I want to measure from CAD, and they all appear as blue geometry in the right place on the CAD. 

Once the part is available I add a manual alignment to the program before the DCC alignment, I then do the manual alignment and the Reference Frame moves to where the part is. If I then do a Sync CAD, the model moves to the Reference Frame, but none of the programmed features move with it. 

What do I need to do to get the programmed features to move with the CAD?