There is obviously more to this story than has yet seen the light of day.
For some reason, this DOT order does not appear to have been referenced in the original FERC recommendation (http://www.ferc.fed.us/RP00-241-006-09-23-02.pdf). That is most likely because it was never introduced by the defendants.
The defendants, El Paso and its subsidiaries, did claim in the trial to have often pumped at MAOP. So either they were violating one order by pumping too much, or they were violating another regulation by pumping too little.