There should be a separate job step for the Notes Databases. Is this completeing OK? If so, you should be covered.
In the flat file backups (C:. D:, E: etc) the Notes database files will be skipped due to what Veritas calls Active File Exclusion, and this will NOT be reported in the job log! See http://support.veritas.com/docs/259152 to turn off AFE to get a flat file backup of the databases