[originator]

Each time I try to ref home, Z goes first, then Y, but Z doesn't make it because a limit switch is cutting in and out. The circuit uses the same input for all 3 switches, so the others are still too close.

Is there a way to back off the switch just a bit more? Homing works fine with the so-called software supplied by the manufacturer.

[Bloy2004]

Possibly try setting a high(2000) in the "debounce" under configs/logic.