This bug was fixed in the package compiz -
1:0.9.2.1+glibmainloop4-0ubuntu11

---------------
compiz (1:0.9.2.1+glibmainloop4-0ubuntu11) natty; urgency=low

  * debian/patches/18_really_fix_stacking_issues.patch:
    - hopefully, this time, the invisible window is dead (LP: #709461)
 -- Didier Roche <didro...@ubuntu.com>   Fri, 11 Feb 2011 13:00:01 +0100

** Changed in: compiz (Ubuntu Natty)
       Status: Fix Committed => Fix Released

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

Title:
  semi-random invisible window with x geometry on top layer possible,
  all viewport only (one ws though)

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