Here's a crappy workaround for people on 'classic mode' that have the
problem.

Launch skype
Open applications - terminal, and type: killall gnome-panel

This fixes the problem for Skype and Shutter, not sure about other apps
that use the notification area.

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

Title:
  1 pixel icons in notification-area-applet for qt softwares

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