I’m using a three pane layout with the inspector open as well, every pane manually resized. If I have Automatic Quit active, then when the app shuts down it seems to lose the window settings. Same if I close a project. Only when manually closing a window with Command-W does Scrivener seem to retain the layout.
Is there a setting I have not found? The old Preference settings seem to have a setting for ‘locking’ the window layout, I think, but I can’t find them in 3.3.6 .
Many thanks.
There aren’t any known bugs, or limitations, that would cause the results you are seeing. I would suspect there is something wrong with that particular project’s settings. Try this checklist, and see if it clears up the problem. If it does, then you could try applying the Layout it advises creating first, to get your settings back.
Thanks for the reply. I’ve been messing about with layouts and trying to figure out in my mind why themes and styles don’t do what I expect. And searching for answers often points to Scrivener Preferences, but they have gone. So I’ve been saving as theme and loading settings from preset and downloading your Butterfly Theme to copy its layout and I guess that in the process I must have done so many things that I ended up confusing the app and myself. 
I’ve since saved the project as a new file, and this seems to have cured the issue. Your checklist is also very welcome.
One thing remains, though. I work on two screens. MacOS 13 on a MicMini M2. When I quit the app on one screen, it always starts up on the other. But fortunately, the layout, including the widths of the panels, opens exactly as how I left it.
Thanks again!
Robert
All right, glad to hear you got things sorted one way or another. 
As for monitors, I don’t know if software is supposed to be making that decision. That strikes me as something the window manager (or the Mac, if you prefer) should be deciding, or if it provides you with some control, your use of that. I haven’t used multiple monitors on a Mac in years, so I don’t know for sure if there are some tricks or settings that can make that nicer.
And searching for answers often points to Scrivener Preferences, but they have gone.
If you are new to a Mac, know that you will probably often come across articles, documentation, tutorials and such (for all software) that talk about “preferences”. Apple decided it would be innovative to change the word to “settings” a few years ago.