Just managed to resolve this for v11d as follows:
stop all backup exec services
logon to backupexec sql server instance using Microsoft SQL Server Management Studio Express
expand bedb database
browse to dbo.jobs table
open the table
select the job record that cannot be duplicated
goto linkedjobid column and replace value with 00000000-0000-0000-0000-000000000000
close the table and mssms express
start the backup exec services
you should now be able to duplicate the job
The issue seems to occur because during the copy process the linkedjobid is copied also, rather than being blanked.
HTH.