Are you sure your mount for the z-probe is thight enough to reproduce the height exactly ?
When I used a printed mount for my z-probe with a clamp in fixing, my height also was changing.
After using a metal mount system with having the z-probe screwed to it, the height is realy reproducable .
You already mention you have variances in about only some 1/100 mm.
The remaining factors are heat elongoation and the bad results when I hit the bed with the nozzle for some reason.
