As of v9.0, Backup exec will skip all Exchange, MSSQL, Sharepoint and Domino files using what it calls "Active File Exclusions" see http://seer.support.veritas.com/docs/259152.htm. These files will be skipped with no entries in the job log.
The only way you can backup Exchange without using the Agent is to shut down Exchange and do a flat file backup (usually not an option)
I guess you could also run NTBackup on the Exchange Serve and backup to disk the Exchange databases and then grab the BKF files with a flat file backup.
As it is, you are SOL as far as Exchange backups are concerned