I'm very sure that the Gov't knew where he was all along. They just waited till now to get him to avoid making him a martyr.
There is still one question that has gone unanswered: How did the Govt Identify him so fast without knowing something about those attacks all along?
Even before the second building fell, the govt was already on TV screaming that they had identified him. If they could gather enough intelligence reports to Identify him that fast, they should have been able to use those same reports to go after those hijackers and stopped those attacks dead in their tracks.
Bush was asked these questions by reporters from the International Media (especially Iran), and bush never gave an answer. All the way to the day he left office, he never gave an answer