I had this problem occasionally before but over the past few days it is happening all the time. I either have to bring up the menu or, if during a cutscene, hit the Windows button to show the task bar, then go back to the game. Never had anything like this in DAI so it seems to just be an MEA issue.
Patch 1.09, Win 7 64-bit.
This kind of issue is almost always related to a background task taking focus away from the active application. I used to have it a lot with BF2 several years ago, and had to prune Windows to make it stop. Alt+Tab or Alt+Enter to switch to desktop and back to full screen will normally fix it.
First I suggest a clean boot procedure (google for guide). Then run the game and see if it still loses focus. If it doesnt, its a program you have causing it. If it still loses focus, its likely the mouse driver or windows power settings.
