Probably need a refresher:
PP, using Finding Corner, set work origin. probe finds xy zero. Jogging confirms center of probe is centered. Changing to a tool, when I jog, the zero is the center of the tool, not adjusted for its diameter. I have the correct diameter and offsets and milling parts are accurate.
What have I forgotten?
If I do the same for z and change the tool, the tool end does zero on the part…
Assumes you are measuring the tool length somewhere (ETS, caliper/block setup or other method) and have the correct tool length in the tool offset for each tool.
It doesn’t sound like you are forgetting anything. What do you think you are forgetting? 
Thomas,
The center of the spindle should correlate to the XY 0 no matter which tool is in the spindle, I’m not sure where the confusion is.
Thank you,
Norman
The confusion is with me. I was shaving the side of a block and was thinking the machine would zero on the OD of the tool. My appologies.