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I dont see this behavior of the calibre window disappearing when you click another window, with the system tray icon off. Not being an OS X guru I don;t have any insight into what window manager settings could cause this behavior.
When you have minimized to tray the only way to restore the window is by clicking the tray icon. That is the way system tray icons work. It's weird on OS X because of the dock, as I said before.
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