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Preferences depend on whether a project is open or not, and whether a project has its own prefs or not (new projects).
Generally, a project will always hold its own prefs. You open a project, and it will look and behave like you set in ITS prefs. However, if you create a new project, it will inherit the last used preferences, which most likely are those of the last opened project.
But you should also be able to set prefs without any project open. These should then be used for any new project you create, like a standard, regardless of previously opened projects. There might be some hickup here...