Spindle position in Axis does not reflect spindle position on machine in space

Summarized Problem: Why doesn't the orientation of the spindle in the AXIS GUI reflect the actual position of the machine's spindle in space? Within the bounding box. The bounding box dimensions and size are correct. 
 
In our Linux CNC configuration when we turn on the machine and open AXIS, the GUI displays a 3D bounding box built by the min and max values given for the joints/axis in the INI file.  The GUI then puts the virtual spindle in the center of our workspace which is fine initially however our HOME position for our Bostomatic 3-axis milling machine is in the top front corner. I was expecting that when we press home all then the GUI virtual spindle will realize it is not in the correct position, however it does not, after it homes the virtual spindle is in the same position in AXIS  as when the application opened (the center). Where as our machine correctly went through the homing procedure where the soft-limit switch and home is shared and the actual spindle is now in that top front corner (which would be the top front corner of the GUI bounding box if it did what I wanted it to).  In this config the min and max values for the x, y and z axis are respectively (-9,9), (-6, 6) and (-6, 6). Which makes sense why AXIS is assuming that the origin, (the (0,0,0)) is the same at the home position.  So then I thought the solution would be to change the x, y, and z axes' mins and maxes to be: (-18, 0), (-12, 0) and (-12, 0) so that the (0, 0, 0) position is that corner where the home actually is.  This does put the virtual spindle in the right position. However this messes up the range of the axes because is assumes the position the machine is in when it is turned on IS on the edge of the bounding box and therefor won't jog in the positive direction because AXIS thinks it has no room but the machine indeed does. And therefor the GUI and the machine are still not on the same page just off in a different way.  SO, how do I get AXIS on the same page as the machine.  

Here is my ini file