If they are only flickering on/off when the axis are at their respective home positions then it would seem to me that the triggering is unstable (bouncing), if they are flickering on/off all the time then it would be noise. However if the latter was the case then Mach would likely see the home signals as soon as you told it to look for them, by homing, and the axis would not move much, if any, before home was set so I think the unstable triggering is the more likely.
Hood