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[Devon <devonfyson@xxxxxxxxx>]

This used to not be an issue in previous versions of Ubuntu. Has been for at least the last couple of versions.
I have exactly the same symptoms as original poster.
Problem occurs when setting shortcuts in either keyboard:shortcuts or in ccsm (compiz): general: commands

Tried changing settings in ccsm: general options: focus & raise
behaviour and found that turning off 'focus prevention level' allowed
for gedit and nemo to open in the foreground even with previous
instances running. However not sure this is a proper fix since without
modifying this, the behaviour was inconsistent (ex shortcuts to genome-
calculator could bring up multiple instances in the foreground, but not
with gedit or nemo), and this may allow unwanted popups in the
foreground such as system updates.

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https://bugs.launchpad.net/bugs/1330889

Title:
  Keyboard shortcuts open window in background

Status in Unity:
  New
Status in unity package in Ubuntu:
  Confirmed

Bug description:
  Hi,

  When opening an application through a keyboard shortcut I defined (of
  the sort Ctrl+Alt+[some letter]), it often happens that the
  application is opened in a window that is kept in the background. The
  phenomenon happens every time with certain shortcuts (those pointing
  to thunderbird, firefox or a custom shortcut to nautilus in a specific
  folder), never with others (custom shortcut for gnome-terminal in a
  specific folder), and "depends" with yet others (it seems that a
  shortcut to Gedit will pop up nicely in the foreground if gedit is
  closed, but otherwise will open a new document and keep the gedit
  window in the background).

  The phenomenon happens on two fresh installs of Ubuntu 14.04 LTS. It
  basically kills all the interest of defining efficient keyboard
  shortcuts. Does anyone know how to fix this?

  Thanks.

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