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Auto-leveling works but nozzle hits the bed

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I have a cartesian printer, with an inductive sensor and an aluminium bed for z probing. Auto leveling and storing it in eeprom with G32 S2 works in the sense that the Z axis corrects when it moves in X and Y. Probing is done for a 5x5 grid over the entire bed.

However, when I start a print the nozzle is too close to the bed. I have measured the correct value of z_probe_height, it's 0.8mm. But when I use this value the nozzle will touch the bed. Even when using a too low z_probe_height value of 0.1 mm the nozzle will still be too close. 

I have run some tests and after a G32 probing session I move the nozzle towards the bed at multiple points. When it hits the bed at any point the Z height is 0.4 instead of 0. Since the value is consistently 0.4 everywhere I think the leveling works. But off course it should be 0, so something must be wrong with the offset between the nozzle and the probe. 

I could try to use an even lower value of z_probe_height, a negative one but I feel this is not a proper solution. What is going wrong here?

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