I have the same behavior even using Metacity: it changes nothing if I
change from Compiz to Metacity using the Compiz Fusion Icon. I followed
the steps on comment #40 but nothing changes. I have four icons on my
notification area: Dropbox, Wicd, Skype and Compiz Fusion Icon.
Sometimes the Skype icon appears when starting the computer, but if I
close it, the only way to make it reappear is by removing the
notification area and adding it again.

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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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