There are certain folders within the /home/username directory that will be skipped during the bacukp procedure. This is because they would either cause loops (backing up the backup) or for the case that an account is inside a chroot jail and does not need all of the copied binaries and libraries to be included.
The list of skipped folders from the User's home directory is as follows:
backups user_backups admin_backups usr bin etc lib lib64 tmp var sbin dev
Data within these folders (eg: /home/user/var/*) is not included in the backup. This can be used to your advantage if you wish to have data in the User's home but do not wish to include that data in the backups. You could create a symbolic link to it from within the public_html, for example.