For a long time I’ve noticed that if I have two separate Firefox windows open (not tabs- windows), one will be in the foreground and the other can’t be clicked or changed. One has the focus, the other is untouchable until the first has been closed. I’ve put up with the issue, but then when I started using Thunderbird again ran into the same issue. I was writing an email and suddenly the main window had focus and nothing I could do would change it and allow me to type my message. So I started looking for others with the same problem.
I found a solution on the KDE forums. I know- maybe you’re not using KDE. Even someone there mentions it should probably be posted elsewhere- it’s not a KDE issue. It’s a problem with an app installed in Ubuntu and probably its derivatives called unclutter, which simply hides the mouse cursor if you’re not using the cursor. Somehow this well meaning app was killing my window management!
The fix is simple. You’re going to edit the file /etc/default/unclutter and change
EXTRA_OPTS="-idle 2 -root"
to
EXTRA_OPTS="-idle 2 -root -noevents"
You will have to restart the X11 server- I just rebooted. Haven’t run into the problem since and the unclutter app still works.