This option isn’t saved between sessions or projects.
In my tests Window > “Keep Quick Reference Panels on Top”, the status is kept between Scrivener restarts. The option is global for all projects. Can you please share more details.
Every time I start a new project I have to reselect the setting. I may be wrong about it not persisting between restarts. I can’t check that bit right now.
This is intended behaviour. The option is saved per project.
If you wish to have it automatically set for each new project you create, you could set it on and make a project template. Future projects using that template would keep that setting.
Wanted to update that this setting isn’t persisting between restarts.