First thing that jumped into my mind was an auto level issue. Watch your printers auto level arm as it runs the auto level sequence... if the "sleeve" the arm slides into is moving(even just a little) when the probe hits the glass the measurements will be off.
If you notice the sleeve moving, or even want to check, then read the next paragraph.
The sleeve is connected to the carriage with two screws that go into brass inserts. One screw is to the right of the arm and visible. The other screw is behind the arm when it's in the sleeve. Unscrew the tiny screws holding the endstop onto the arm. Then slide the arm down and out of the sleeve. Unscrew the two screws holding the sleeve to the carriage. Check to make sure both of the brass inserts are there. Our Workbench was missing the "hidden" screw insert, which caused the sleeve to pivot, just a little bit, around the other screw whenever the probe touched the glass.
FuseBox 1.5 CoreXY - e3dv6 - Graphic Smart Display
Solidoodle 2 - e3dv6 - Hobb Goblin - e3d Titan - lawsy carriages - Direct Drive Y Axis - T8 Z axis - OctoPi