So I just upgraded our control PC to a new one. Windows 10. Meh.

Anyways. 2006 PRT Alpha. explor control board. Everything seems to be working. But when I zero wth my x axis with my zero plate, it runs through my C2 command, but then my control software reads 1.0" and when I look at my bit to my table, it's only at about 1/2" up. Any ideas?