I've confirmed that this is NOT just a problem with VirtualBox, per this
comment:

"I suspect this is also part of a few other less prevalent glitches that
occasionally happen when switching virtual desktops."


There is another common glitch with Unity, this probably applies to all 
programs, but I most typically see it in Firefox.  Occasionally, when 
right-clicking on a link, the context menu disappears as soon as I try to 
mouse-over onto it(it seems to happen sporadically after switching virtual 
desktops, more infrequently than VirtualBox).  Also, whenever the context-menu 
problem is present, if I type into the URL text box, it does not suggest URLs 
that I've visited before as normal.

I've determined that this is part of the same problem as VirtualBox.
Whenever the bug is present, if I re-focus the Firefox window by
pressing ALT+TAB, the bug goes away.  This indicates to me that the
problem is related to the Window not properly receiving focus after
switching virtual desktops.

Can somebody please edit "VirtualBox" out of the title of the bug?  I
think we can confirm this is a more general and widespread bug now.

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https://bugs.launchpad.net/bugs/778578

Title:
  Problem with window focus when switching virtual desktops when using
  VirtualBox-OSE

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