Sorry for the bump but this thread is top of a Google search result. Can you be more specific as to which of cpbackup and backup is legacy and which is the new backup system?
Also is there any chance you could update WHM to explicitly state which is which?
"Backup" refers to "/usr/local/cpanel/bin/backup" and is the new backup system. "cpbackup" refers to "/usr/local/cpanel/scripts/cpbackup" and is for the legacy backup system. You can actually leave both cron jobs enabled, as the scripts will determine if backups are enabled and generate them as needed.