Sorry if this is a known problem/feature/beaten topic, but I couldn't find anything about it in the wiki or the forums.
There seem to be some discrepancy between the mouse coordinates returned by system->get mouse X and the mouse cordinates used by then mouse/keyboard object.
The system event seems to be using the game window coordinates (0=left of game window) while the mouse/keyboard object seems to be using the whole screen coordinates (0=left of screen).
I think this is a good way of generating confusion, and why isn't there a setMouse X/y action in the system object in the first place, if there is a get mouse x/y?
If you can read the mouse position you should be also able to write it from the same object IMO.