Setting Junction Deviation in firmware has no effect
I've bought an SKR Pro V1.1 which is suffering from the same problem. It has actually to do with a shortcoming or design flaw (of the "HAL" or "Hardware Abstraction Layer" addressing of SPI devices) of Marlin and access to the SD card; I quote:


  The problem: On board SD-Card on SKR-PRO 1.1 can't be used. 


After the SD card has been inserted, the firmware binary is loaded into memory, and all access to the SD card is gone. The initial connection is by hardware design of the SKR boards.

Basically, there is a bug in the Marlin code/SKR boards preventing storing (to the SD card) any alterations after the firmware is loaded. There is a PR on Marlin that fixes it, but it has not been merged into Marlin yet.

There are 2 options, 


Every change to the firmware has to be compiled and uploaded to the board by placing a hex (firmware.bin) on the SD card;
Compile a firmware version from the sources from the fore mentioned PR.