I just switched my vanilla Ender 3 Pro board out with a BigTreeTech SKR Mini E3 v2.0.
The first thing I tried was auto home which sent the unit all the way to the right of the X-axis, making a lot of noise and then I got the message that the homing failed.
I checked all my connections again, same result.
I then tried moving manually along each axis from the Move menu; turning the knob on the display right would send it in the positive direction and left would send it in the negative direction, as expected, for the Y and Z axis. But for the X axis, either turning the knob left or right would send it further to the right (away from the end stop switch).
I switched back to the original board and everything worked fine.
I switched to the SKR and the problem persisted.
I tried to swap the X and Y connectors on the board and then the Y axis behaved as described, meaning the problem is on the board, not the wiring.
I ran the original firmware, Bugfix 2.0.x and then tried flashing to 126.96.36.199 with the same result.
I have seen the red jumpers on the board mentioned in some posts. None of those are present on the board.