I run a bed leveling script that hits Z0 at the center point and right below each X, Y, and Z tower. This works well, and is how I've set my stop screws, delta radius (horizontal radius now), and other calibration bits...
If I run a script that hits Z0 at the points in between each tower (indicated by A, B, and C in this picture) my head is perfect at the center, but about 2mm above the build plate everywhere else.

If I run a script that goes X, A, Z, B, Y, C (around the perimeter clockwise [that's anti-cyclonic for Gene]) The head will go back and forth between the perfect level point and the 2mm high point.
WTF?
I recently did the V1 to V2 conversion, and the problem followed. I was also concerned about the flatness of my build plate, so I switched from cheap window glass to a real borosilicate plate.
So the wood is all new, and so is the build plate... What am I missing?