Only in the folder tree, or in the file display as well for the same folders?
What do you see in File Explorer's folder tree for the same locations?
How are labels involved here? Those could be messing up your icons. What is your label setup?
Edit: Based on what you mentioned in Separators between Favourites in Folder Tree - #12 by wickett, I'd say your labels are clearing the folder icons entirely. But it depends what those labels are assigned to.