The following is from someone close to Zinni:
I agree that Holbrooke orchestrated, along with [Bill] Burns and DirGen of the Foreign Service to overrule Clinton. And that is what happened. She actually shook hands, said "welcome aboard" etc so that is no chance that there was a miscommunication. Jones, as we see, is just a person who handles mechanics.
And this from a serious observer:
What's most interesting about this is Holbrooke wielding influence on one-off issues like this. Conniving with Burns and the DG under the Secretary's (and Steinberg's?) nose is pretty impressive. They may have been making the argument that [we] need to have senior FSOs somewhere, a point Burns and the DG would hve strongly agreed on. The Hill appointment can be seen as a victory for the service which is otherwise getting flushed by this admin so far.
I wouldn't have expected Clinton to get rolled so easily. But that seems to be the story, with Obama playing almost no part in the selection of what is surely America's most important diplomatic post.