Status:
Issue fixed in SQL Server plugin version 11.2.
The latest version of the NetVault Backup SQL Server plugin can be downloaded from:
https://support.quest.com/netvault-backup
Workaround:
1) create separate Backup Jobs for each one of the SQL Server instances
or
2) Instead of selecting the instance and crossing databases (excluding manually), consider to select at the database level, the databases that the end user wants to include in the backup. I.e., just select databases to backup, rather than select all and then exclude some.