When you setup the job on your machine the XY datum must be in the lower left corner of the material
That wasn't something I was aware of but I always use the bottom left hand corner when setting up any job so nothing different for me
You only set your X, Y zero once when setting up the material on the machine, after that it should never be altered as highpockets has said. Z axis is obviously different because you will be doing tool changes
Not checked your file but does the horizontal trench
appear in the toolpath preview ? If so could it be something you have selected accidently when calculating the toolpaths. if it doesn't then that is something that might worry me a bit.