Several people stated that the previous job zero is in memory between power cycles. So if your previous job was 1/4 inch and you zero’ed Z on top of the 1/4 inch project, until you rezero the relative Z zero is at 1/4 inch above the spoil board no matter which tool you load. So if you power on your machine and the router comes to the front and asks for a tool and you put a new tool in the BitSetter sets the new tool for 1/4 inch above the spoil board. So after initialization, BitSetter and the router comes to the front use your “Load New Tool” button, the router will ask for the tool and then after “Resume” it will set the new tool but it will still set the zero for the last time the z zero was set which was 1/4 inch above the spoil board.
Then jog and set your zero’s with probe or paper method and if the new project is 3/4 inch the new zero for Z will be 3/4 inch from the spoil board if your project uses the top to set as a reference. Any tool you put in the router without rezeroing will set it at 3/4 inch above the spoilboard.