What is the difference between CAD Transformation and CAD Positioning?

[[An...]]

In the CAD>Modify CAD Entities window there is a "transformation" tab and a "positioning" tab. Both allow you to rotate and move the model so is there even a distance.

I am having a very frustrating issue where my model and XYZ triad are correct but the CMM itself moves the opposite direction on each axis, when the "show probe object" is on I can see it move Z- when I am jogging the machine in Z+

[[Ma...]]

For me - tranformation is only used - positioning is something like moving one object to another by clicking, i am not familiar with it.

Your problem: you probably have a bad features used in base alignment. By "bad" i mean features which are known for acting up while manual aligning. So problem can be solved by doing manual alignment again, or using better features ( aka 2x circles instead of 1 cylinder for rotational axis )

[[No...]]

Positioning is only used in Planner to place the model(s) on the granite of the virtual CMM, so you can reproduce the situation on your physical CMM with all the mounted part fixtures, pallets, calibration spheres and so on for collision detection.
It has more options for placement like clicking a point at the bottom of the model and one on the granite to move the model straight there and to the correct Z height.