Here's a Manual Homing sequence that works and is repeatable.
First - Jog all axis near (less than 1 ") the "Home" position. Tap the <TAB> key to bring up the Jog Pendant, change Jog Mode to Step and distance to 1".
Select an unused offset, On the offset screen type in 239 for the offset and make sure all values are 0 (zero)
I start with the Z axis - I now hit the Jog Z Up key and wait for the Z axis to hit the limit switch and stop moving and the E-Stop is flashing. Reset teh E-Stop. on the MDI Screen type G92 Z0 and the DRO for Z will read 0.0000. Now zog the Z axis away from the limit and wait for it to finish moving 1".
Now repeat for each of the other axis.
I do this on a KX3 and have very repeatable results.