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I have a three axis router with 6 limit switches that I wired together down to three pins. when I check the switches in the diagnostics tab, all three pins are lit up in green. Is this what I want or should the be normally off? I notice that im not able to assign the home switches to a pin, I set the number, hit enter, and it goes back to zero. Any Ideas?

The limit switch virtual LED in the diagnostics should be off (grey) when the limit switch is not active and should be on when the switch is active.
If it works in reverse then change the Active low checkbox of the limit input pin.

If the software does not allow you to set a port/pin number for an input then it is because that pin does not exist or that pin is not an input but an output.
A usual mistake with the AXBB-E controller is that it has the pins labeled I1, I2, I3 etc. which means Input1, Input2 and Input3 etc. and not 11, 12, 13.
So, sometimes users missread this and using the wrong pin numbers.