Look for code in the custom class you're using, that eats. Maybe it's overriding HonorBuddy's eating routine. Any eating SHOULD be preceded by a check for the 'Food' aura - if you have it already you shouldn't attempt to eat, because that means you're already eating.
I know I have a custom food eating bit in my class, and I can see where if it was done wrong (or WoW removed the food aura!) that it would exhibit the symptoms you said.