Sebastien, what makes you think that the bug is not related to gnome-
panel?

Given the fact that

  gconftool-2 --recursive-unset /apps/panel ; pkill gnome-panel

fixes it, makes me believe that the bug is triggered by some panel
settings and therefore by the behavior of the panel.

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Panel utilities not shown on startup using Matrox gfx
https://bugs.launchpad.net/bugs/572550
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