While your design problems manifest themselves in the middle the error might have occured earlier.
Say Y axis is told to move 10" away from you but for some reason it bump into something 9". So when the Y is asked to come back 10" it overshoot by 1".
But your machine is loosing steps, question is why.
Make sure your $1=255 and that the Xcontroller board dip switch #4 is set to OFF.
This disables any torque reduction functions for your machine.