If I have multiple projects open in tabs, often when I quit Scrivener, it only closes one of the projects, instead of closing all of them and quitting Scrivener.
I think this behavior only started once I upgraded from Sierra to High Sierra.
Are you sure you are not hitting Cmd-W (close window) instead of Cmd-Q? The quit behaviour is all down to macOS, so there’s nothing in Scrivener controlling this.
All the best,
Keith