Hello, I used to suffer from the same focus issues, this is why I waited a 
little bit for the qt5 switch.
Since the latest vbox releases (maybe after 5.1.10 or so) I don't experience 
such issues anymore, can you please try again with the repo version?

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https://bugs.launchpad.net/bugs/1673463

Title:
  VirtualBox grabs focus, causing issues in GNOME Shell and Unity (other
  DEs might be affected too)

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