I think this would be due to what's called Active File Exclusion, which basically gets Backup Exec to automatically skip those files which it assumes can't be backed up since they would be in use, eg database files. I don't use Domino so can't be sure it's the same, but it certainly is for SQL Server.
Have a look at http://seer.entsupport.symantec.com/docs/242688.htm for more info (relates to SQL but the same should work for you with Oracle) and how to turn it off.