Ok I tested several times with one game, and different games, both on LB and BB, it seem to occour randomly, most of the time the screen appear. What I can think of I changed on Cemu settings was starting full screen, and remember window position, but I turned off and it didn't help. My Cemu is on an external SSD, so don't need to run as admin then.
I also tried to change my controller combo to bring up the pause screen, thinking it could be some kind of conflict, but it didn't help either. This just happens with Cemu, I think started with one of the lasts updates, I also changed the pause screen theme, could be this?
Just remembering, this happens when I try to exit the game through the pause screen (for now exiting pressing esc on the keyboard allways works), I don't have a key bind on my controller to close active window.