When you say you save the individual folders, what are you doing exactly?
Do you have entries for the folders under Preferences / Folders / Folder Formats, in the Path Formats section at the top?
When you open a window, where does the format lock say the current format is coming from? [See #6 in the guide linked below.]
How are you opening the window?
If you haven't already, it's worth reading the Folder Formats: Detailed Guide.