GPO Preferences are blank in comprison reports
If GPOADmin is version 5.2 or newer then confirm the OS version that the GPOADmin server is installed on. GPO Preferences were new as of Server 2008, therefore if GPOADmin is not installed on 2008 then the reports will not show preferences. Even if the report is being run from the GPOADmin console which is running on 2008, and the GPOADmin server is on 2003, it will not show the data as the report is actually generated from the server.
If GPOADmin is version 5.1, this could be defect TF00146752 which was resolved in version 5,2.