Fred, you are right of course, but the underlying issue is well known.
The X Window specification lets an application "grab" the mouse pointer
or the keyboard, preventing any other application from using them until
they are released again.  Like many things in the X Window System, this
only works if the application behaves itself and doesn't have a bug in
the wrong place.  There would probably be ways to work around this - X
has a "give me back my mouse" key combination which you can activate -
but fundamentally this can only be changed by replacing X with something
else (Wayland?)  And hoping that the replacement doesn't have any
equally silly problems that no one thought of in time!

Take a look at http://www.x.org/wiki/Development/X12 if you are
interested in other shortcomings of X11.

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https://bugs.launchpad.net/bugs/603482

Title:
  Desktop freezes if new window takes focus while menu is open

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