I have now found a solution to this issue. It seems that I have a
hanging glxinfo process which seems to halt the startup of many
programs, including metacity.

I have in my initial state 100% CPU usage which is consumed by Xorg and
glxinfo. Just by chance I ran 'glxgears' to see if I had good 3D
performance. It immediately made glxinfo quit and metacity etc.
immediately started and everything was back to normal.

So by running glxgears I crashed/ended glxinfo which made the desktop start 
continue again.
 

** Changed in: mesa-utils (Ubuntu)
Sourcepackagename: None => mesa-utils

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Top panels doesn't exist on any windows until I do 'metacity --replace'
https://bugs.launchpad.net/bugs/188389
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