The same problem appears when I open a file in Gedit with gksu, eg.
"gksu gedit /usr/share/applications/gedit.desktop". See screenshot.
Using sudo is no problem, though.

Gedit 3.4.1-0ubuntu1
Unity 5.12-0ubuntu1.1
Ubuntu 12.04

** Attachment added: "gksu gedit.png"
   
https://bugs.launchpad.net/gedit/+bug/965510/+attachment/3162433/+files/gksu%20gedit.png

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https://bugs.launchpad.net/bugs/965510

Title:
  option --new-window not working correctly

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