I had the same issue in Ubuntu 14.04.1 LTS. 
Another situation to reproduce the problem is: on the keyboard, press the 
Calculator Button (keyboard shortcut). It'll open in background.
I fixed this problem with the answer available at 
http://askubuntu.com/a/130349/154850.
Hope to help someone else.

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https://bugs.launchpad.net/bugs/781931

Title:
  New windows are moved to front but don't take focus

Status in Compiz:
  Fix Released
Status in Compiz 0.9.8 series:
  Won't Fix
Status in Compiz Core:
  Confirmed
Status in GTK+ GUI Toolkit:
  Invalid
Status in Nautilus:
  Fix Released
Status in Unity:
  Invalid
Status in Unity 2D:
  Invalid
Status in Unity Distro Priority:
  Fix Committed
Status in compiz package in Ubuntu:
  Fix Released
Status in nautilus package in Ubuntu:
  Fix Released
Status in unity-2d package in Ubuntu:
  Won't Fix
Status in compiz source package in Precise:
  Confirmed
Status in nautilus source package in Precise:
  Fix Released
Status in unity-2d source package in Precise:
  Won't Fix

Bug description:
  Impact:
  sometime new dialog doesn't get the focus

  Test Case for the nautilus SRU:
  - open gedit, click in the text entry
  - click on nautilus on the launcher
  - check if the nautilus dialog got the focus or not

  Regression potential:
  nautilus could steal focus when it should not

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