Hi, Jeff
Have you tried reducing Velocity and Acceleration Settings in Motor Tuning, Use G00 moves to set it up.
If I understand what your saying, Your at x0, y0 making positive moves and on return the machine is moving to a more negative position each time,
But Mach indicates x0 y0 home position ?
If your Velocity and Acceleration Settings are to close together, Decelerating to late and slipping past the x0 y0 position is possible.
Let us now, More info on your mill, ver of Mach3 (Under Help About), May Help.
Thanks, Chip