Could be number of things but why your most likely getting this happening with IP-M and not other boards is because of the speed and sensitivity of the IP_M I/O. It's much much quicker than most others to reacting to signals however the down side is that it's less tolerent of bad wiring or Dodgy switches etc.

So this could be number of things and difficult to advise with accuracy without seeing more or being in front of machine.

I'd start by putting the Signal filter back to default = 1. Shouldn't need this and I've never had to raise this on any machine even when using cheap mechanical switches or prox switches. Having set high will drasticly slow down the reaction times but more importantly will mask any real issues.

Next I'd go back to the start and trace all wires to make sure none lose or shorting etc. Then check the switches closely, swap over to other axis and see if moves etc.
The IP-M is rock solid with noise so i'm confident it will turn out to be wiring or switch at fault.

Sorry can't helo more than that.