That's probably because the apps are launched by gksu, and bamf doesn't
handle that well.

** Package changed: unity (Ubuntu) => bamf (Ubuntu)

** Project changed: unity => unity-foundations

** Also affects: bamf
   Importance: Undecided
       Status: New

** Changed in: bamf
       Status: New => Confirmed

** Changed in: unity-foundations
       Status: New => Confirmed

** Changed in: bamf (Ubuntu)
       Status: New => Confirmed

** Summary changed:

- Unity Bar problems with the application icons for applications run as root
+ Bamf issues with matching applications run as root

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https://bugs.launchpad.net/bugs/778828

Title:
  Bamf issues with matching applications run as root

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