Note the publication date (9/11/06) of the article, Are Fake Videos Next? Video fakery theories concerning 9/11/01 were already out there at the time, but as yet lacked the force of argument they gained with the release of Simon Shack's September Clues in June '07.
Hany Farid could perhaps resolve these questions once and for all with the video forensic tools he has developed. A quick search however finds no indication that he has publicly addressed the issue. If he has examined the alleged anomolies in question and found nothing, certainly we would have heard about it. But if he found something, it's not likely to be broadcast. He doesn't seem the type to jump in with the truthers... So get him good and drunk at a reception, then maybe he'll tell.