Thanks for reporting this bug and help to make Ubuntu better.
The main menu is an indicator, and so, not in the system tray.
I think it's more an appmenu issue than unity one, put the package task
as invalid as of now and let the appmenu dev to state and debug it.
** Changed in: unity (Ubuntu)
Status: New => Invalid
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Systray icon menu is overridden by main window menu
https://bugs.launchpad.net/bugs/657855
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