Never mind the post above, I had to enable named pipes in the SQL Server Configuration Manager.

Also, I noticed that I get a duplicate key error with named server instances when running the report of missing database backups. I made the following tweak in bold to the first step of the SQL Agent job to correct this :

INSERT INTO [rep].[Database_List]

([Server],DatabaseName,Usage)

SELECT [Database_Status].[Server]

,[Database_Status].[DatabaseName]

,isNULL([SSIS_ServerList].[Usage],'NA')

FROM [Database_Status] INNER JOIN [SSIS_ServerList]

ON [SSIS_ServerList].[Server] = [Database_Status].[Server]

Where NOT EXISTS (select * from [rep].[Database_List]

WHERE [Database_List].[Server] = [Database_Status].[Server]

AND [Database_List].[DatabaseName] = [Database_Status].[DatabaseName]

)