I only had the problem with gedit as root too. 
As normal user the menus are showed in any case from the first installation, in 
gedit and nautilus. Nautilus as root shows menus inside and only in gedit as 
root has no menu with any appearance configuration I choose. Perhaps is not de 
same bug.
Is someone who has solved his issue installing the new packages experiencing 
problems with gedit as root?

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https://bugs.launchpad.net/bugs/1532226

Title:
  No menu bar in gtk apps on fresh boot

Status in Release Notes for Ubuntu:
  Fix Released
Status in bamf package in Ubuntu:
  Fix Released
Status in bamf source package in Xenial:
  Fix Committed

Bug description:
  Seen here in fresh 16.04 install using 01/07/16 image.
  Around 35% of fresh boots or restarts results in no menus in unity panel for 
most apps, notable exceptions are firefox & thunderbird
  A log out/in restores functionality.
  When this occurs there is nothing in any of the ~/.cache/upstart logs of 
obvious note

  Test case:
  fresh install, no changes
  Do a number of restarts from system settings, using either restart > restart 
or shutdown > restart, here randomly picked one or the other
  What happens here: 
  around 35% of the time the login has no menus in the unity panel for most 
apps.

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