If you launch Audacity (one and only one Audacity window), set the window size and toolbar layout as you want it, then close Audacity, the window size and layout should be remembered the next time you launch Audacity.
Having said that, why do you need to have 9 windows open at the same time? Audacity is a multi-track audio editor, and in nearly all cases only one window needs to open at a time. It looks like you have adopted a seriously non-optimal workflow.
It’ll only save the layout when the last window is closed. Perhaps you had a window behind the other windows that didn’t have the new layout (?). I’m just guessing and we will probably never know what actually happened 
If you describe in detail, what you are trying to do, we may be able to suggest a better workflow.
If you want to apply the same effects to a load of files, then the best way is to “batch process” with a Macro.
You can find out more about Macros here: https://manual.audacityteam.org/man/macros.html
A good tip for finding things in the manual:
Go to the manual’s index page (https://manual.audacityteam.org/), and use your web browser’s search function (usually “Ctrl + F”).
Example: Try searching the index page for the word “batch” and you will find it.