The working area includes the distance the machine is able to move forward off the spoilboard so as to be able to interact w/ the BitSetter, see:
for some discussion on this.
It looks like you were trying to take more off than the endmill which you used could comfortably remove in a single pass — best way to do this is to start cutting at the highest point, removing only as much as is necessary to allow the endmill to cut reliably, and to increase the depth by that amount for each pass until one surfaces the entire area.