I read the Fox News article you linked to and if you read it closely It said he took the plane he usually takes. It is very possible he does not go in the Presidential Marked plane most times. When he was done in Iraq and got back to DC he then boarded the AF1 to go back to Crawford.
Go to posting #1579. TexKat posted an article that gives the information I told you I heard.
It makes a whole lot more sense then to think he took the AF1 that has all the Presidential markings on it into Iraq.
Here is a snippit:
"Instead, Bush had quietly slipped away from his home on Wednesday evening, in an unmarked vehicle and wearing a ballcap pulled down low over his forehead. He flew to Andrews Air Force Base outside Washington accompanied from Texas by two reporters and a few photographers summoned only hours before. There, he picked up a few aides and some more reporters sworn to secrecy, and made the switch to another plane inside a huge hangar for the long flight.
It was evening in Baghdad when the president's plane — which had flown the whole trip with its lights darkened and window blinds closed — landed under a crescent moon, with Bush himself in the cockpit to watch Air Force One pilot Col. Mark Tillman "bring it in."
Air Force One landed in darkness at Baghdad International Airport. Security fears were heightened by an attack Saturday in which a missile struck a DHL cargo plane, forcing it to make an emergency landing at the airport with its wing aflame.