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I figured I would go and check on the ticket.
It was closed with a note that explains how to fix the problem:
Go to Preferences->Interface and enable the system tray icon. then --start-in-tray will work. --help wont work on windows as windows doesn't support console output from GUI executables.
So, basically start Calibre like normal and select the option in Preferences screen. Close Calibre and then start it from the command line with the --start-in-tray option and it'll run in the tray. You can even click on it to access the gui and "x-ing" out of the gui will keep it running in the tray.
Mitch
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