This may well be an issue between Compiz and Nautilus. When Nautilus is restarted (try it yourself: killall nautilus), the same delay can be observed. But this happens only when Nautilus tries to draw the desktop; when Nautilus isn't running, invoking it with 'nautilus --no- desktop' doesn't cause the delay. Maybe it's related to how Compiz handles the root window? I am just guessing.
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