Hi there,
do you use a BedLevel Sensor? As far as I know, this is a known issue with the SKR Board.
I currently use a SKR 1.4 TURBO with a capacitance sensor for bed leveling. Without this sensor activated in Marlin, my mechanichal endstops are working.
When i activate the Bed levelsensor, my mechanical Z-endstop stops working though i can see the current state in malin with M119.
Maybe you should first test the state of the endstopps with M119 to see what's happening.
Greets,
2bbionic