G54, and really ALL G54-G59, is the distance from machine coordinate zero to work position zero. So if you set G54 Z0 to some number, say your 4.3118, they MDI in G0 G54 Z0, the machine moves there. Clicking the Machine Coordinates button will alternately show 0 and 4.3118.
Homing in place I don't do and don't know how it really works. Having limit switches eliminates that, machine coordinate zero is always the same place.
The really odd thing here is one tool runs fine and the next "sometimes" does not. Are both roughing and finishing passes using the same tool?
Another thing, in a "normal" situation, with Z homing at the "top", all the way UP, and Z direction set right, G54 would be a negative value.
Tom