You should be able to look at the gcode file in repetier host or the estlcam preview and see if the tool paths move on the second pass. If you were really clever, you could find the positions of x, y at the corner in the gcode and see if it’s offset on the second pass.
It might also be that you are losing steps, so when the tool is going down the right side, if it loses steps, then it would start in the wrong spot in the upper left. A rectangle would help, so you could measure each side, and see if it’s skipping. It seems like the left side would be messed up more than that though.