When you use javascript moveTo(50,50); for example the window moves to the correct position in most cases always on the main monitor (the one with the menu) and oddly enough also on the second monitor if it is placed to the left, top or bottom of the one with the menu. However if your second monitor is placed to the right of the first one (my set up) when used moveTo(50,50) the window is moved far right almost off the monitors right edge.
Does no longer happen with latest nightly build ;-)