Some people at Symantec did care enough to get in touch with me and help resolve a problem that as it turns out plagued both Darren and I.
Thanks to Russ and Ron for their help.
The issue was after installation you want to set up your backup for Domino.
But when we would go to click on the list of Domino databases, well you clikc on the drive letter first, it would never come back and show the list. Eventually you have to exit or stop the processes and that got annoying.
What took 4 months+ to figure out is there was a file in the wrong place on the server.
The ndgts.dll file which should be found in c:\lotus\domino was in c:\lotus\domino\data incorrectly.
What we both found was we also had a version in the correct place. the correct version was in the correct place, but the incorrect version, which looked to be from Domino 8.5.2 or 8.5.0 must have been installed incorrectly during a fixpack update or some other way. Maybe my IBM support friends will have some insight.
Deleting the file from the wrong place, rebooting the physical server(to clear the dll from memory) allowed the process to continue.
As Russ said on the comments to the other post:
It turned out in both cases that there was an older Domino DLL (NDGTS.DLL) in the Domino data folder that the Backup Exec agent was finding before getting to the proper version in the Domino binaries location. Have a look here for the resulting fix Technote. http://www.symantec.com/docs/S:TECH164926
Thank you to Symantec again.