It sounds like you're losing steps. This happens when stepper motors try but fail to reach a commanded position. In an open-loop stepper system, there is no feedback mechanism to compare the commanded position to the position actually achieved. But it will be evident when the tool is moved back to the original zero position - the DROs will say it's at zero, but the place will be different.
The first thing to do is to check for mechanical problems. This might be a sticky place in the slides, a slipping pulley, etc. If that's not it, then usually adjusting the velocity and acceleration settings will fix the problem - if the velocity is in a reasonable range, reduce the acceleration by half and retest; usually it will behave better. Of course, there are other things that will cause lost steps, but try these first and let us know what happened.