I have the same: ATI card with Ubuntu 10.4. Some icons appear, some do
not, like "Desktop", "PulseAudio", and "Terminal". Without open-gl
everything is being displayed. Sounds like a problem that is simple to
repair when root-cause is identified.

-- 
Cairo-Dock Applets are invisible in openGL mode
https://bugs.launchpad.net/bugs/581350
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