Mine was making the noise, only when getting off the accelator pedal. Took it to the dealer, they gave me a print out of a bulletin from Ford saying the noise was normal. Funny thing is, it has never made that noise since I got it back from the dealer! (knock on wood).
They told me it is acceptable and printed out bulletin for me, It is #18845 and reads
"Flutter noise on deceleration
Some vehicles equipped with a 6.0l diesel engine may exhibit a flutter type noise from the air box/intake area on deceleration. This noise typically occurs when decelerating after heavy acceleration. The noise is a normal characteristic of this engine and has no impact on engine or turbocharger durability. No repair should be made for this condition. Effective date: 09/21/2005"
Had 21k miles on it at that time.