Hi,
It seems that you are performing a backup using the AOFO option and some files are getting skipped.
Kindly make sure that you are not performing any Database backups while using the AOFO option as this is not recommended.The database backups have their own database agents (Like Exchange and SQL) to take care of the online files.
The AOFO should be used for normal files on the system.
Kindly refer the following technote,
http://seer.support.veritas.com/docs/263784.htm
However If you are doing a normal file level backup using the AOFO option and are getting the files as skipped then kindly send or include the abstract of the job log showing the files that are skipped.
This would help us to diagnose the issue better.
-Also confirm that AOFO is properly installed.
Further also check the following technotes,
http://seer.support.veritas.com/docs/253620.htm
http://seer.support.veritas.com/docs/253620.htm
Hope this helps.Feel free to revert back with further queries and necessary information.