Having multiple windows is indeed a feature which can be found under File->New Window.
If this happened by accident you may have accidentally hit the key binding for opening a new window.
Thanks for getting at my issue so quickly and resolving my mystery. I shall feel a bit dumb not to have found it again.
In one of my environments (Windows 10, DbVis 13) I managed to create two main windows. Is this a documented known feature or a glitch I found and cannot reproduce?