There is no problem running Alltray from the command line. The bug
happens when using Alltray "visually", when it offers the option of
clicking the window you want to tray. When the Desktop Effects are
activated, Alltray can not find any window to tray. Running Alltray in
debug mode gives no useful info.

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No windows hiding with compiz
https://bugs.launchpad.net/bugs/106583
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