I think what was happening was that calibre started up and initially displays the menus / columns that are used with NO device detected. Then, the device detection occurs and the menus switch to the ones used WITH device detected.
You can customize both sets; when in Preferences select Toolbar and then in the dropdown list you will see "The main toolbar", "The main toolbar when a device is connected", "The menubar", "The menubar when a device is connected". As the descriptions suggest, one set is used WITH NO device attached, the other WITH A device attached.
All pretty straight forward once you know how it works.
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