Autoleveling issues: Printhead too high

Hello everyone!
I'm having trouble getting autoleveling to work on my Prusa I3 but I didn't see any topic discussing my particular problem.
I'm using an inductive sensor attached to the printing head using it as a Zmin endstop as well, the bed is aluminum and I'm using Repetier Firmware 0.92 and Repetier Host.
The problem is that whenever I send the G32 command to do 3 point, software Z correction the head is constantly a couple mm higher than it should be, no matter where I position it.
My guess is that the rotation matrix gets translated upwards, I say this because when I home the Z axis after probing I can see the head going down to the correct height and then go back up.

Changing Z probe height in EEPROM doesn't fix it, sending G92 doesn't fix it.
I tried adding a fake, uniform bending correction in EEPROM to see if I could get around the problem with it but it didn't help

A thing I noticed is that when the printer finishes G32 it gets to the center of the bed and sends its position back to the command terminal, but Repetier Host still thinks it's at X and Y home and Z10 (as I have to lift the head up before issuing G32 so as not to trigger the probe before it reaches the first point); which means I have to home everything a second time.
Could it be that the machine and the host have different origin points?
Could it be the "Z_PROBE_BED_DISTANCE" setting screwing everything up?

I'd like to stress that when homing Z without autoleveling enabled the head is at the right height, it's only after it probes that the problem occurs.
I'd also rather not having to use a Zmax endstop because it would take ages to reach.

Thank you in advance for your replies.

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I'm using Repetier Firmware 0.92

1st off i would recommend using the dev version of firmware,it has been greatly improved in the levelling section.
try that and see if the problem is sorted.

Allso, G32 S2 will store the levelling matrix into eeprom.

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st off i would recommend using the dev version of firmware

It made things worse. Now when I issue G32 it decides to go on an adventure mid way through probing and it tries to measure outside the bed.
Also, when I tell it to home Z it runs around the print bed for 20 mins and doesn't even add the probe height.

I forgot to attach the config files before, let me fix that.

ok, some things i would change in the dev config

Homing order use Z up X Y preheat Z
Your P1,P2,P3 probeing points did not make sense

I have made these changes in the attached config. give it a try and report back.

after uploading new firmware dont forget to update eeprom with
M502
M500

It didn't help. In the dev version homing seems to be broken because the head changes XY position mid way through Z measurement. I tried uploading your config.h with the dev version as well as using it with the 0.92 version, as well as changing manually my previous 0.92 config to match what you pointed out, but the result is still the same.

Have you tried G1 x0 y0 z0.
Is the printer in the fron left corner? this shoul be the coordiante center.

If not. maybe y endstop and direction of the wrong coordinate are inversed...