I'd be willing to bet more than a dollar that there is a hell of a lot more to this story than what is being reported. And unless John tells his side of the story, I doubt we will ever know for certain exactly what prompted him to leave.
Ok... you are correct. Wikipedia didn't list him as coordinator for his second stop at Southern Cal but the USC website lists him as the Defensive and Recruiting Coordinator/Defensive Line coach.
Someone on twitter said that Chavis used to be a Miles guy, but when Miles brought in Cam that they sort of 'alienated' themselves and it pissed Chavis off. And now Chavis feels disrespected over the money, and clause in his contract.