Bug#432802: compiz: Compiz intereferes with workspace switcher and window selector applets
Unfortunately, compiz is not part of Gnome, so I don't think we can
expect it to look as well integrated in Gnome stuff as Metacity or so.
You might want to look at compiz-fusion anyway, since this is where
actual development is done now, and I don't expect many improvement in
the plain compiz in the near future regarding these problems.
By the way, why do you use multiple workspaces instead of a single one
with multiple faces of the cube? Is there any interest in using compiz
without the cube effect?
Brice
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