I had also thought that In the Heights was the strong favorite that year, but the New York Times poll that year showed that Passing Strange actually had received more votes in their poll. The poll that year was smaller than now and got a number of predictions wrong, but it was presumably a close race.
That was one of the first years that they published the poll before the end of the voting period. I wonder if the poll results influenced last minute voters at all. I guess we will never know. I really wish the Times would wait a day to publish the poll.