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I was wondering what was meant by the system tray icon as well. System tray is enabled on my system, and I don't recall ever enabling it, so I assume it's a default setting?
Anyway I see the window disappearing behavior very intermittently - I've assumed it was something to do with Spaces or Expose - a lot of applications can behave a bit oddly with those features, I wouldn't be surprised if QT based apps are in that category.
One thing (I've only just learned) that's nice about the system tray is I can close the window using the red 'x' and restore it - I wasn't aware of this. Without the restore option in the tray I don't see any way to restore a closed window - neither the dock or the Calibre menu have an option to open a new window.
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