Frustrated that it wasn't getting its way with the judge (a circumstance that prosecutors rarely encounter), the government tried to recuse her. Prosecutors thought Judge Shira Scheindlin created an appearance of unfairness by noting in an article that judges had a duty to protect individual rights after 9/11. The Second Circuit was unmoved by the argument that a plea for fairness is unfair to the government.
Some jurors in the first trial seemed eager to convict a defendant named Osama. The second jury, perhaps taking a more dispassionate view of the evidence, apparently accepted the defense perspective:
Mr. Awadallah’s lawyer, Jesse Berman, countered by saying that his client never meant to give the grand jury wrong information, and did so only after enduring 20 days of incarceration that left him confused, frightened and paranoid.
Many thanks to a TalkLeft tipster for calling attention to this article by Ethan Leib, which advocates a "reform" of the jury system by eliminating the requirement of unanimity in criminal verdicts. Unanimity, like proof beyond a reasonable doubt, provides protection against wrongful convictions.
A majority vote may be more "democratic," as Leib asserts, but jury deliberations aren't elections. Juries bring democracy to the courtroom by acting as a check against prosecutorial power. If the government's evidence isn't persuasive enough to convince twelve people, the government shouldn't get a conviction.
Awadallah's case demonstrates the wisdom of the unanimity requirement. Contrary to Leib's argument that unanimity prevented a fair verdict in Awadallah's case, the second jury's verdict suggests that the lone holdout in the first jury had the most reasonable view of the evidence -- a view that prevailed in the second trial. In any event, it's difficult to argue that an 11-1 conviction would have been the "correct" result when a second jury was so quick to return a 12-0 acquittal.