The "grey window" was from the same profile (actually I only have 1 - I created another to try some time ago, but have never used it).
I am referring to the "Bookmarks Bar", which I can toggle on/off from the "View" Menu.
Now, when I access through the "Bookmarks" Menu the "Bookmarks Toolbar" seems to have my new bookmarks, but the "Bookmarks Bar" does not.
I had always assumed these were the same; in the past editing "Manage Bookmarks" has changed the "Bookmarks Bar", but they seem to be different entities. Ideally I would like the "Bookmarks Bar", which I use the be the same I manage with "Manage Bookmarks".
PS Just checked the Preferences, and the "Bookmarks Bar" was set to "Bookmarks Toolbar" . I toggled through a couple of other settings, then back to "Bookmarks Toolbar", which seemed to resolve the issue.