Handbrake used to be able to put AC-3 passthrough in my .m4v containers no problem...now whenever I want to put an AAC pro logic II file in first and a 6 channel discrete AC-3 passthrough second it never does it! Literally I am so pissed because I'll waste 6 hours on a BluRay encode only to learn I only have a decent copy with Pro Logic II...I first noticed it when I converted The Hurt Locker it added two Pro Logic files....so i figured no big deal I have an Mkv file of it...tried it again and it did the same thing. Now if I do it with any other movie it just adds the Pro Logic first and no AC-3 passthrough even if I use the Apple TV present and touch nothing! Its annoying! I'd like to be able to have more compatible files since NO ONE supports Mkv in the devices like the iPhone, Xbox360 (oh God how I hate the Xbox360's media player), etc. Anyone have any advice?