Well, started having issues when I fired it up today. Doing the same thing it was. It's like it isn't even trying to home the slave, the diagnostic light for the slave lights up before the master, but the slave doesn't stop until the master does.
I swapped the wires for the X (not the master) and the A, the X homed fine, slave did the same thing. Swapped the actual switches from Y to A thinking maybe one of my hall effect switches was bad, no change.
Messed with it bit longer and it suddenly starts working. I have also had the e-stop trigger for n o reason a couple of times, so I may have a noise issue. Though the Y and A switches only get near any other wiring right where they connect to the mx4660. All the grounds are bonded my motor cables and limit switch cables are shielded. Only thing I can think of to try, is powering the input opto isolators with the same 12v supply the switches are powered with instead of the internal one on the mx4660.
I even tried upping the noise cancellation in mach 3 to like 10000. Didn't seem to effect it, it just seems to work sometimes and not others.