We just ran into this issue. Turns out that an errant automation script wrote bad records out, causing the GTM to fill up our disk space with errorinf directories. Thus preventing the zone files from being updated. We had to delete all the directories under /var/named/tmp. Another indicator were database error messages on the GUI performance screens as RRD couldn't update it's files either.
It would be nice to see an DevCentral article on how the GTM synchronization / zrd / named process occurs. We have had a few issues where making updates too quickly or in the wrong order got us into trouble.