This also affects me.
I've found that sometimes clicking between desktop and windows makes them show 
up again.
Also switching between desktops sometimes wakes it up.  But it's definitely a 
weird and frustrating bug to experience.

* Ubuntu 12.10
* nvidia-experimental-304 (304.48-0ubuntu1)
* xserver-xorg-core  (2:1.13.0-0ubuntu6.1)
* compiz (1:0.9.8.6-0ubuntu1)

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https://bugs.launchpad.net/bugs/952887

Title:
  Transparent terminal windows and black backgrounds in other windows
  after kernel update

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