I've noticed even when I type "hostname" at the CLI the FQDN is displayed, however the only file that seems to be using the short name is /var/log/messages. I'd prefer it to use the FQDN however I can't seem to figure out how to do this.
What do you have in your /etc/hostname ??
Try changing it and run
Additionally you can try adding only a FQHN reference in your /etc/hosts: