I seem to have found an alternative workaround. In gnome-tweaks  (advanced 
settings) , under Desktop, choose "have file manager handle the desktop" to 
"off". It seems to me that this makes the invisible windows bug to disappear. 
The price, I guess,
is that you do not have icons on the desktop anymore. But you can use nautilus. 
And dont have to do the "killall nautilus" routine.
For some this might be less annoying workaround.

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https://bugs.launchpad.net/bugs/876999

Title:
  compiz doesn't show any windows with VirtualBox guest additions

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