Hey guys. I am also affected by the bug and I am using unity. A
temporary workaround that works for me (at least with disappeared skype
icon) is killing compiz: killall -9 compiz. Hope this is helpful to
someone, before a fix is released.

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

Title:
  1 pixel icons in notification-area-applet when compiz is the windows
  manager

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