Problem also occurs here on KDE : all the windows disappear until I
right-click on the desktop and open the "run" window. Then, when I open
a popup menu that covers my kicker window, all the windows disappear
again until I re-open the "run" window.

It's tied to compiz, since when I deactivate it everything becomes find.

My config :
- Gutsy with latest update.
- Athlon 64x2 3600+
- NVidia 7900 GS

-- 
[MASTER] broken initial stacking (was: compiz hides quick loading windows at 
login)
https://bugs.launchpad.net/bugs/147943
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