The following simple commandline-tool remultiplexes MP4-files using the old Nero syntax for AC-3 (at the implementation time there was no related ETSI-standard) to such using the new ETSI-syntax:
http://www.nero.com/redir.php?id=4568
Hope it's useful.
(Please note that in the remultiplexed file Nero 8 ShowTime might not anymore recognize the AC-3 audio track. If you are a Nero 8 ShowTime user, you should keep the original file)