These days having "excess" content directories shouldn't be an issue - when DS searched for textures that weren't where the library file said they were having more content directories meant slower searches, but now DS always prompts you if the file path isn't correct. If you have auto-refresh on in Edit>preferences?Directories that might be the problem - try turning the option off (you can always force a refresh by clicking the triangle button at top-right of the Content palette and switching to another view mode, but you need do so only if you add new content while DS is runnign and want immediate access)/