Why does your Doc Admin need access to Source and Published folders? If tasks are properly defined, nobody really needs access to the Published documents folder. Only QVS does.
Usually, you put different documents under control of different groups of doc admins in different folders in different trees, e.g. C:\docs\A and C:\docs\B, NOT C:\docs\A and C:\docs\A\A2. If this isn't already the cause of your problems, please specify what your current Source Folder Paths are, and what your are trying to define as a separate source folder for your new doc admin (and that is causing the duplicates to appear). Or post screenshots of QMC->System->Setup->Distribution Services->General and QMC->System->Setup->QlikView Servers->Folders.