I have the same thing with Eiskaltdc++ Qt.
It seems that this bug affects all QT applications which minimize to tray.
The workaround with "killall notification-area-applet" works, but it takes two 
or three times to run the command for all the icons to appear in the tray 
correctly.

** Also affects: eiskaltdcpp (Ubuntu)
   Importance: Undecided
       Status: New

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https://bugs.launchpad.net/bugs/767095

Title:
  1 pixel icons in notification-area-applet for qt softwares (e.g.
  Skype)

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