Probably you have bind-chroot installed and /var/named/chroot/etc/rndc.key is missing or it's usage misconfigured. But how to know if you present no real data about your configuration.
I was caught by surprise when I first discovered the chroot setup after an upgrade, and did some head-scratching when edits to /etc/named.conf only affected initial loading. Then I realized what was going on and changed the files in /etc to be symlinks to the "real" files in the chroot directory at /var/named/etc.
