I had a similar problem, but mine was constrained to the Y axis. The gantry would move along then stall while the stepper was making a sound like the screw was at its limits. I solved this by mapping the Y axis to the unused 4th axis on the card. (very easy to do) This worked for a while, however, as of today I have a call into excitech to see why the problem is occurring again. I went so far as to replace the ballscrew, as it seemed like a mechanical issue. It was not.