Did you use a new Blank Project, or did you use a template? Many of the templates include their own preferences, which will override the system-level defaults.
I used the choice that says “Blank,” but it doesn’t specifically say “blank project.” If you go to “new project” you get a dialogue box that gives you choice of templates, and one says “blank.”
Hmm. On my system the Blank project does indeed take on the system-level settings.
Are you working off a Dropbox volume or removable media? I’m thinking perhaps the system preferences file might not be available when you create the second project.
Another thing to check would be to see if the new project really does have the system preferences that it’s supposed to. So look in Scrivener -> Preferences while the new project is up and see what it says. If some settings are missing, you might look in Project -> Text Preferences for the project that is set up the way you like it. It’s possible that you changed some settings at the project, rather than the system level.
If you tend to use a variety of different formats, it could be worthwhile to create your own templates. Set a project up the way you want and use File -> Save As Template.
And to add to that, all of the templates should use your global formatting settings by default. Some have been configured with some sensible Project/Text Settings overrides, but these are disabled, specifically to avoid confusion. So under no circumstances should any of the built-in templates, and especially Blank, be using formatting settings other than the universal defaults. I second the suggestion to double-check those. Perhaps you had to revert settings at some point and they are no longer what you thought they were. Easy to fix though; just load up an older project that has correct formatting in it, and use that to pull into the universal defaults with that handy button.