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I don't normally use the tray icon myself. I think it is disabled by default when run from the .desktop file due to being "horribly broken" (in Fedora anyway).

So I'm testing it out now with Audacious as another icon in the tray and I can't easily reproduce any problems. I think it disappeared when first run, but works on subsequent runs.

Do you use beryl or compiz for desktop effects? Can you provide steps to reliably reproduce the tray icon's disappearance?