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1b1ed1a
(Get the code!)
After a while playing with this problem, I have got it down to be an annoyance, rather than a showstopper.
Not being a Linux guru, my opinions are of limited value, but I firmly believe this is an X-Server/XOrg problem. I've seen it happen under GNOME and KDE, and with all combinations of window managers, and decorators.
There appears to be a connection with ALT-TAB ... as soon as the mouse focus issue happens, you lose ALT-TAB.
Anyway, I have discovered that if I activate ALT-TAB as soon as I login, it seems to "protect" my system, and I don't seem to lose mouse focus.
I have also discovered, that CTL-ALT-D (show desktop) seems to recover mouse focus ... once all windows are minimised to the taskbar, then ALT-TAB seems to work again, and mouse focus is restored. Hopefully this workaround will prove useful to people, and can remove the need to logout/login again, or to restart the machine with the loss of data that implies.