I have an issue I think is similar, though I do not have the ATLAS.
After homing the machine, and selecting the part file, I touch off on the corner of my stock. When I hit the start button, it prompts to insert first tool, which I have already done before touching off (how would you touch off without a tool inserted?). I click through that box and then the router starts, moves to the correct X,Y origin where I touched off, but does not plunge far enough to actually touch the material before moving along the cut path. I stop the process, hit start again, and then it returns to the part origin, and then plunges to the correct height before starting the X,Y movements of the cut path. What am I doing wrong?
Also, are the set origin buttons along the right side of the window supposed to do the same thing as the set origin buttons on the left? Here again, when I have tried to use the buttons on the right, the machine does not move to the correct Z height before starting along the cut path, and I have to use the buttons on the left.