I'm having the same issue. I think it is a notification. I haven't completely stopped it, but usually it happens when some program decides it wants to be upgraded and so it puts up a notification and that notification takes over the screen. It's a complete pain in the butt and I wish programmers wouldn't write programs whose upgrade notifications might interfere with other programs, but I think they think their program is the most important thing in the world...(sorry for the rant, but seriously, programmers, write programs that are more well behaved.)
Adobe programs are extremely bad in this regard. Acrobat is usually a culprit, but SuperantiSpyware was the worst. It just wouldn't quit. It would put up a notification to update, take me out of the game screen to the desktop (and I die) I would close the window, go back to the game and a couple minutes later it would through up a notification again, take control of the screen back to the desktop. I eventually uninstalled SuperAntiSpyware and it's a little better.
What is truly odd is that I turned off all notifications in the Win settings, but it still happens. Even programs for which I specifically turn off notifications.
I don't know exactly where the solution is, but I'm pretty certain this is a flaw in the way Windows 10 handles notifications. For some reason they think all notifications are so important they will interrupt and interfere with anything already running.
I hope someone comes up with a fix.