If you are in a Windows network, you can use Active Directory groups as accounts in your section access, for example. QlikView respects the permissions in the operating system, so say you have two QVW files, one has full access and the other is restricted to "Sales" Windows NTFS group. When a user from group "Accounts" logs in, he will see the non-restricted file only. So check your NTFS permissions in each file or folder in the Root and Mounted folder and assign permissions accordingly.
Hope that helps.