I think this is being triggered after certain package upgrades - I
upgraded some gnome-related debs (not incuding gnome-shell) a bit before
and I just noticed this happening now.

Perhaps a post-installation GConf hook is causing the GConf client in
gnome-shell to break?

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https://bugs.launchpad.net/bugs/853582

Title:
  gnome-shell apps overlapping over wrong activities desktop

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