Hi Scott,
Micael has the correct instructions and just to add a bit more detail, to get into the CNC interface go into the Conf. tab of the software UI > Server > Linux CNC Server Web Configuration. To change the X offset go into axis 0. If you're off by 0.5mm or 0.02 inches, then change the offset by 0.01 (half the total offset), save it. Go into 'system' tab and restart the CNC and Rockhopper, refresh the software and then try. If it's off more, change to 0.01 in the other direction and see if that helps.
When working through this with Micael, we took a piece of 1 inch delrin stock and drilled 1/2" into the stock, rotated 180 degrees and drilled 1/2" in the other side. It was with a 1/8" tool, and so when we put in a 1/8" dowel pin it did hit in the middle, but I could push it all the way through with just a bit of force and couldn't feel a shelf or ledge with a tool. Ultimately, it seemed like a slight tolerance stack up, but it wasn't such a large shelf that we couldn't get the 1/8" dowel in to the other side.
We'll look into why this issue is happening a bit more, since we're not sure why after the machine is calibrated it is off by so much in these cases. We check the homing repeatability in all axes 10 times to ensure that both the home offset is set correctly and within a certain tolerance. We also cut a square on a 1" piece of delrin and measure it in X and Y and make sure that the block measures within 0.001 inches although this doesn't address the rotation of the B axis and then repeatability of the X and Y.
Please let us know what you find.
Thanks,
Kerry