Ian,
So you should create new report, enter name for it e.g. "Library Files", View type e.g "List", fill in description field e.g. "Organization filter do not work here. If it works then you don't see files that belong to null organization", select report type as "Organization Filter" and paste edited query, then press save. In the query you should replace all values in <> brackets and remove brackets. If you have any questions regarding this please ask them.
Query itself:
SELECT
RIGHT(F.Handle, CHARINDEX('\', REVERSE(F.Handle))-1) as "File Name",
LEFT(F.Handle, LEN(F.Handle)-CHARINDEX('\', REVERSE(F.Handle))) as "File Path",
O.Name as "Owner Org",
F.FileSize as "Size in Bytes",
F.FileDate as "Last Modified",
SC.LastUpdateOn as "Last Deployed GMT",
SC.Name as "ServConfig Name",
AC.Name as "AppConfig Name"
FROM
<vcs_db_name>.<auth_usually_dbo>.T_File F
LEFT JOIN <vcs_db_name>.<auth_usually_dbo>.T_Organization O ON F.OrganizationId = O.Id
LEFT JOIN <vcs_db_name>.<auth_usually_dbo>.T_MountPointConfiguration MPC ON F.Id = MPC.LeafFileId
LEFT JOIN <vcs_db_name>.<auth_usually_dbo>.T_ServerConfiguration SC ON MPC.ServerConfigurationId = SC.Id
LEFT JOIN <vcs_db_name>.<auth_usually_dbo>.T_AppConfigServerConfig ACSC ON SC.Id = ACSC.ServerConfigurationId
LEFT JOIN <vcs_db_name>.<auth_usually_dbo>.T_AppConfig AC ON ACSC.AppConfigId = AC.Id
WHERE
F.Handle like '%<distinctive_library_path_we_use_hosting.surgient_here>%' /* AND
<vcs_db_name>.<auth_usually_dbo>.T_Organization.Id in (?) */
ORDER BY
RIGHT(F.Handle, CHARINDEX('\', REVERSE(F.Handle))-1),
F.OrganizationId,
F.FileDate
Regards,
vadym