Hello BCMaint:
Do you have home switches installed ?
It sounds like you are not using home switches to set the "machine reference zero" positions on the machine.
There are two sets of axis data. One is the "machine coordinates", and the other is the "work" coordinates. The work coordinates are the G54 .... etc.
Example: X axis has a "reference switch" when the machine spindle is at the far right end of the table travel, but just short of the limit switch. When this switch is tripped during "Ref X", the dspmc will set the "machine X Zero coordinate to 0.000., and move off the switch the amount set in the "ports and pins" limits section.
This table has columns for all the axis, homeing in the + or - dir, active high or low, reference rate, distance to move off switch, etc.
The dspmc "Config Plugin" has a box to check on the right side of each axis page, for the Index channel on the encoder.
After all the axis are referenced, you can set the G54 home for x,y,z anywhere on the machine you choose; then when you "Goto Zero", the machine will move to the G54 Zero positions for x,y,and z which are relative to the "Machine Home x,y,z.
The dspmc controller has inputs for the reference switches.
Hope this helps.
John