I've also had this problem from time to time, but I'm not sure whats going on, or if its problem with the icon area itself (aka KDE and GNOME)
** Changed in: amarok (Ubuntu)
Status: Unconfirmed => Needs Info
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Freedesktop Notification Area Icon is often displayed in the wrong place in
GNOME.
https://launchpad.net/bugs/74219
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