You have to set your work offsets for the stock you have. Make sure that the file loaded is calling the same WCO that you are currently in. I wrote up a detailed discription here: Z shifts and crashes with PCNC770 - new to CNC stuff - #2 by Davie
Here is a video primer on work offsets.
more videos you might like are here Video List - Chapter 1 - Getting Started with PathPilot