When you open a document from a network location in Adobe Reader XI there is, depending on exact details, a 'Security Warning' dialog that asks you to 'Allow' or 'Block' the file. If you open the file again the dialog is not shown so the file name is stored somewhere but not in the 'Privileged Locations' settings.
Where does Adobe Reader store the list of files that have been 'Allowed'? Alternatively how can I find out what files/settings have changed when I click 'Allow'.
Note that the trusted folders/privileged locations are stored in the registry here: HKEY_CURRENT_USER\Software\Adobe\Acrobat Reader\11.0\TrustManager\cTrustedFolders but that this particular dialog does not alter these settings.
To reproduce the exact problem use a Windows 7 PC with Adobe Reader XI. Create a mapped network drive that maps to a shared folder on the same PC with full permission for Everyone (e.g. M:\ maps to c:\AdobeTest). Put on FDF that links to a PDF in the folder and open the FDF with a command line or shell from an application.