I managed to narrow it down to Unity being the main cause of the issue.
Compiz with Gnome Classic is not affected. The problem exists only when
Unity plugin is active in Compiz.
** Also affects: unity (Ubuntu)
Importance: Undecided
Status: New
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https://bugs.launchpad.net/bugs/929712
Title:
Missing context menus for Qt apps after minimizing the window
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