If I have more that three or four apps open at one time, all of the
non-active windows will pop open at random and predictable times with
the result that no one window will be useable, unless I close every app
that's open.
- sticking keys on keyboard generating some sort of keyboard shortcut to show all windows?
- hotspot on your screen to show all windows?
- glitch in your DE? Try a different Desktop Environment (Icewm instead of Gnome, etc).