@Phaedrux
Thanks a lot for the help.
I actually went through that tutorial before.. but, now it just works.
Didn't have to change a line and was few hours on that already,
I have no clue what happened... but happy o/
Never mind, i figured it out. The reprap firmware configuration assistant was using M208 to set the minimum z height to 1mm. I changed it to 0mm and now when i run the calibration I'm getting 0.1mm as expected.
To be honest, the configuration assistant was more trouble than help. I'd almost recommend not suggesting it in your documentation.