The original list of hijackers obtained by CNN did not contain Hani Hanjour, the alleged hijacker pilot of American 77. Instead it contained the name Mansour Khaled (sometimes misspelled as "Mosear Caned").
You can find the original discussion of this here:
http://www.democraticunderground.com/discuss/duboard.php?az=view_all&address=125x42650#42972
In relation to this Paul Thompson says:
Late 1998-August 10, 1999
"Pakistani Air Force Pilot Temporarily Replaces Alshehhi as Atta's Roommate"
Hijacker Marwan Alshehhi moved to Bonn, Germany in 1996, and studied German there. He then lived in Hamburg for several months in 1998, and returned to Bonn after failing a language exam. Just as he left town, a Pakistani student named Atif bin Mansour arrives in Hamburg, and begins living and studying together with Mohammed Atta. Early in 1999, Mansour applies with Mohamed Atta for a room to hold a new Islamic study group. Mansour is a pilot on leave from the Pakistani Air Force. As the Los Angeles Times puts it, "This in itself is intriguing--a Pakistani pilot? Investigators acknowledge they haven't figured out Mansour's role in the plot, if any." On this day, Mansour's brother, also in the Pakistani armed forces, is killed when his surveillance plane is shot down by India. Mansour returns home and supposedly never comes back to Germany. Soon afterwards, Alshehhi returns to Hamburg. (Los Angeles Times, 9/1/02) In March 2001, Mohamed Atta applies together with a Pakistani Air Force pilot for a security job with Lufthansa Airlines. This pilot is a member of the same Islamic study group as Mansour, but it's not clear if this is Mansour and he did come back to or stay in Germany, or if Atta was associating with a second Pakistani Air Force pilot. (Newsday, 1/24/02; Network of Terror, 11/01) The FBI later notes that Alshehhi arrived "almost as a replacement" for Mansour. After 9/11, the FBI asks Pakistan if the flight lieutenant and squad leader Mansour can be found and questioned about any possible role he may have had in the 9/11 plot, but there's no indication Pakistan as to whether has ever agreed to this request. (Rediff, 7/17/02) In late 2002, the German Federal Bureau of Criminal Investigations will say that Mansour remains "a very interesting figure." (Los Angeles Times, 9/1/02)
It's my guess that these two people - Mansour Khaled and Atif bin Mansour - are actually the same person; Muslims often have lots of names and sometimes switch between them (Atta's last name isn't actually Atta, which is one of his middle names), so the guy's full name is probably something like Atif bin Mansour Khaled.
You'll remember that ATC Danielle O'Brien, who was on duty at Dulles Airport that day and monitored American 77 as it came in, said that, "This must be a fighter," because it was going so fast and was so manouvreable. However, she wasn't referring to the type of plane, but to the manner in which it was being flown - passenger planes like to give their passengers a smooth ride for obvious reasons, whereas fighter pilots throw the plane about.
So the plane is being flown like a fighter and a fighter pilot appears to be on board. It's a shoo-in that he was flying it, not Hani.
The reason it was covered up is that it would cause trouble with Pakistan and without Pakistan it would be impossible to invade Afghanistan.