I saw this noise issue masked by increasing the input filter time; it was a setting in mach3 called something like switch bounce or low pass filter or or or. find it and increase from default to 10 or 100x bigger; the one i saw 'fixed' made it like 200msec delay which shud still be ok for estop.
real fix is to reduce the spinde drive noise; have u got shielded 4 conductor cable from vfd to spindle motor? shield tied to ground at both ends? motor grounded to that 4rth wire in the cable?