Z location seem to be wrong with auto tool measurement

Hi
I have been trying to understand what causes this issue with QTDragon UI running LinuxCNC 2.10 pre release. 
The issue is, almost always, the Z position seem to be wrong after i enable auto tool measurement.

This is what I usually do:
1. Enter the block height. I either measure this manually or utilize the 'Work Piece Height Probing' mentioned in 14.1 of the manual. This is given in the probe section.
2. I have setup the tool sensor at a given X/Y with search velocity, etc. I have also modified the tool change command to trigger the python plugin which does an automatic tool height measurement with this sensor. The height of the tool sensor is also fixed and given. This is provided in the probe section.
3. Load the gcode program and start. 

It correctly triggers the tool measurement and continues, but almost always the Z height is wrong. What is shown for G54 is unrelatable to the real Z height which should be there for the program. 

Is there anything that I am doing wrong? Do I have to set things up differently when I generate the gcode from Fusion 360? Also I see that some f the parameters like block height, tool height need to be specified in many places of the GUI. Which one is used by the auto tool measurement?

Thanks
Sus