I have changed my original post because I have realised it was something different to what I thought.
I have my scene which handles the onMoved messages. In a child layer I am using Actions to move the child layer.
this.popup.runAction(cc.MoveTo.create(.2, cc.p(-200, gamePopups.defs.y)));
Anyway after using the action for some reason th eonMouseMoved event is not the correct mouse position. It seems to be adjusted by the Action from the child layer.