good test running the 'mfgr servoconfigurator' getting commands via USB to help isolate the problem..... tell us who the mfgr is and what the device is that uses this servoconfigurator program. I assume it is the drive amplifier software but that is just a guess...... if you reply tonight I will use that to make a prediction of where you may want to look.....
2 additional questions: the encoders feedback is using differential sigs (a,a-,b,b-)?
and same question on parallel output from printer port; I assume it is step & dir commands to the drive - so u have step.step-, dir, & dir- hooked up?
3rd question: what is cable from par port to interface card - ribbon cable? shielded twisted pairs? how long? and is it near ANY other wires?
couple more hit me: u sure motor coupling is not loose? something else in drivetrain mechanically loose/slipping?
does the the servoconfig program uses a slower accel rated than the mach3 so it didnt mech slip?
is there a spindle drive on this machine? did u try test with it off (they often cause noise problems)?