i have dealt with those issues before, they were caused by :
1.) my Gecko drives needed to be tuned, which is why I was wondering what kind of motor drives you had.
2.) when I assembled my machine I grounded the motor drive encoder grounds to the cabinet chassis - it caused noise to affect the step and direction signals and stopped after I disconnected the ground.
3.) the acceleration settings in Mach3 were too agressive.
spend some time to find out how your motors are being driven, follow the wires from the encoders on the motors to where they terminate and find out
what that particular unit is and who makes it. Then investigate to see if it can be adjusted I believe the adjustments are refered to as P.I.D. - Integral, Differential and something else I cant remember at the moment. These adjustments had a really profound effect on motor performance.