—UPDATED— So, not sure if I found the problem but since I have the fancy dancy touch probe, I used it. My cuts are now lined up perfectly. So either I have some other little issue of my dang eyes are worse than I thought and I am not lining up the bit to the corner of my work piece.
For this example, I cut a piece of wood exactly 5" x 5". It is positioned at the front left corner of the machine using 4 Oops clamps. In VCarve, my job size is X=5" and Y=5" and Z=.25".
The XY Datum position is set to the lower left and the offsets are set to zero. In Vcarve, I created a .1" circle and a 1" square and centered both using the centering tool. I created a profile toolpath selecting the cut to be on the lines using a #111 ball nose (.0625) end mill.
I initialized the machine and positioned the bit at the front left corner of the workpiece. In Carbide Motion, I selected “Set Zero” and then “Zero All”. At this point, the xyz points all indicate zero.
Below is a download link to the gcode file and the crv file. Not sure if I provided all the info needed. Let me know if there is anything else that would help.