If you set the origin at the surface of the MDF and jog up 1 inch how much does the machine move?
For the BitZero see:
If you still have difficulties with the machine set to have the correct configuration upload a .c2d file, step-by-step notes on how you are securing your stock and managing all tool changes and setting zero relative to the stock and a photo showing an attempt at cutting still in place on the machine with the machine at the zero position or a specified offset.