Hello everyone,
I have been having the issue that whenever i move my mouse from in-game to my second screen in order to control my pop-up navigation map for example, the game still registers my clicks and scroll activity in-game making me accidentily push buttons in the cockpit whilst clicking on the navigation map on my second screen. Basically the game registers clicking and scrolling on my second monitor as clicking and scrolling on my main monitor (cockpit).
Does anyone know how to solve this? I couldn’t find any topic discussing this so far.
I have this issue as well. It’s very noticeable for the Aerosoft CRJ, where the tablet is on the left side of the screen.
When you power off the tablet, move the cursor to the second monitor (on my left side) and click anywhere on the second screen. The tablet boots up again. Indicating that a click on the second monitor, while the Flight Simulator window is active, registers a click at the border of the window. After that, the simulator is not the active window anymore and clicks do not impact the simulator.
I can sadly say I have set my plane back to ‘Cold and Dark’ due to this issue. So far I’ve avoided that by setting the tablet to the Checklist mode, but if this issue could be fixed that’d be even better! 
Also, I’m not sure if ‘Hardware’ is the right category? My choice would be Miscellaneous, but I’ll leave that to the forum moderators.
Has anyone found a workaround for this? Pretty annoying when you’re doing 400 knots and you click on your second screen and your flaps fully deploy, or your gear goes down.
I also have the same issue. Whilst it happens on all pop out windows, it makes using for Instance the Air Manager panel in a Baron 58 G1000, impossible because of the risk of affecting the main screen. This does not appear to be that common an issue in that it has taken me hours to find others with the same issue. Is there a solution or does it need raising with Microsoft / Asobo?
Seem to have solved this. Was using two ipads for additional monitors, running Duet on one and Xdisplay wired connection on the other. For various reasons I have uninstalled these, and the issue has gone.