Your problem actually is a minor one: The green cross indicates where the tool comes from, not where it is going. On startup FreeCAD assumes that the machine's origin is at (0,0,0).
If you look at the GCode with "Inspect GCode" you see the following (I put some comments behind):
Code: Select all
G00 X-0.390000 Y-2.971000 (horizontal movement only, no vertical movement)
G00 Z14.000000 (go to height 14 mm)
G01 F0.000000 Z13.000000 (go down 1mm)
G03 F0.000000 I0.390000 J2.971000 (first circle)
Besides the fact that I think it is somewhat ambitious to start milling just at the workpiece level it isn't a problem, if your machine's initial position is above this level.
You can follow the milling path in the "Inspect GCode" window, when you mark the text from the beginning.
There is another thing which bothers me although I think it is independent of Path WB: Your model is extremely CPU intensive, although the model seems to be reasonable. If I omit the polar pattern and put the holes in the first sketch everything is ok.