This is really so irrating.
I have the same issue.
Fortunately when I use alt+F2 and then type metacity --replace , it is fixed.
I have this every login and also have window border issues with a qt app in 
unity.

When I clicked a terminal to open in the menu, it does not show without the 
metacity --replace command.
A fix would be highly appreciated.
I must add that I use 11.10 Xorg to be able to use nvidia-96 driver.

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https://bugs.launchpad.net/bugs/973559

Title:
  Window decoration not showing up

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