For version 5.1 or later, Linux file permission is also backed up during the backup operation. For other versions, please do the followings:

Add a pre-backup command to dump the Access Control Lists of all files you want to backup into a dump file. For example, if you want to have all files under /home to a /ACL.txt, please add:

cd /; getfacl -R home > ACL.txt

to your pre-backup command.
Add "/ACL.txt" to the [Backup Source] of this backup set