I was thinking about that this morning really. I was fighting an ochu and they're known for handing out afflictions. I bet the chocobo had an affliction so was stuck in combat mode until that timed out. I caught emnity from another while troubleshooting and by the time I fled the chocobo was back to normal.

Honestly, I'm thinking this may not really be a bug at all; just that the companion AI will keep in fight mode as long as it is being injured and can't heal. Similar to how companion/pet AI will attack a pacified target... not really a bug but just a shortcoming with the AI. Anyway, thanks all for helping me figure this out!