I'm not sure what release it changed on, but if you were running AutoCAD on two monitors they used to be completely separate. By that I mean you could open any widow, like layers properties manager, and it would be specifically for that session of AutoCAD and stay on the monitor that you are working on. In effect you could have layers properties manager open for both sessions and on the respective monitor. Now when a pop-up window opens it remains on one monitor, but is shared between two session. Anyway so change the pop-ups to be separate foe each session