Looks to me you have switches that are not detented switches and are experiencing contact bounce when the switch goes to reclose.
IF you get contact bounce even for a millisec MACH will stop as it should and the switch remakes and shows the led as on. BUT the home cycle was completed at the first sign of the switch remaking on the bounce.
That explains WHY mach3 continues ON with the X and Y routine and completes the cycle.
OR that lime peel on your head is causing you to see things

? I normal use a hat made of tin foil and a copper grnd strap dragging on the ground. It kills off all the static.
(;-) TP