I've noticed my Y and X axis are backwards on the keyboard up=down, down=up.
Also when I press ALT to initiate incremental jog, the buttons on all axis are in the opposite directions to when I jog normally, either in slow or rapid.
I noticed in the book it mentions the JOG.FIL can have logic to alter the axis direction, but I don't know either how to enter the logic or even if it can be changed only on the 2 axis.