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Marlin 2.0.5.3 won't home properly

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I bought an SKR v1.3 board a while ago and I got some time now to upgrade my printer. I bought the TMC2208 drivers with it. I am able to get most of the configuration working except for homing. I have enabled individual homing in Marlin. I'm using an inductive probe for homing my Z-axis.

I can home the X and Y properly but while I home Z, this is what happens (listen to that awful grating noise just before Z homing starts). `Z_SAFE_HOMING` is enabled and is set to move the X and Y to the middle of the bed and then home Z (the default state in configuration.h). The full configuration is available here. configuration_adv.h is available here. What am I missing here?

I should also mention that I have de-soldered the R11 pullup resistor for Z-min endstop from the board.

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