Sadly the problem is still there. Rebooted the system without starting
Skype, and as soon as i launched Firefox the invisible window was back.

** Attachment added: "xwininfo output"
   
https://bugs.launchpad.net/ubuntu/+source/compiz/+bug/709461/+attachment/2130626/+files/xwininfo.txt

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https://bugs.launchpad.net/bugs/709461

Title:
  Application windows can sometimes fail to display and will mask
  regions of the screen

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