When I convert some movie's from an .avi file to a .mp4 file so that I can put it into iTunes, I am getting a popping audio sound. On the vast majority of movie's I've converted I haven't had any trouble, but on the Lord of the Rings and Kingdom of Heaven no matter what I do I get the audio popping sound which is so bad that you cannot listen to the movie for more than a few seconds.

The only target format I've found that seems to reliably work with iTunes (so that I can have the movie's show up in Front Row) is iPod MPEG-4 480W. If I play the same movie's in VLC they work fine, no matter if its the original downloaded two files or the file I've joined together using ffmpageX, but as soon as I convert them to MPEG-4 480W I get this load popping sound. Any idea's on what I can do, as I'm running out of options to try. I suppose its not a huge deal as I can still watch the movie's with VLC, but I want them to show up in Front Row/Apple TV so that means converting them to a supported format with ffmpeg. Thank you in advance for any help, its appreciated.