I ever face to your problem when I try to use dual Z independence. I found the solution as below;
Config.g
;Define Axis
M584 X0 Y1 Z2:4 U4 V2 E3
homez.g
G91 ; relative positioning
G1 V5 U5 F6000 S2 ; lift Z relative to current position
G1 S1 V-405 U-405 F1800 ; move Z down until the endstop is triggered
G92 V0 U0 Z0 ; set Z position to axis minimum (you may want to adjust this)
We need setup one more axis and home the individual driver. So it will true independence endstop one each driver.