Hi,
I discussed this issue in the Elgato-Forum, because I use the Turbo.264HD stick to encode video-files in H.264 (great product!!!).
I had the same issue, that files encoded by the turbo.264hd with the AppleTV-profile should include the DolbyDigital-stream, but this stream was not offered or played by the AppleTV2.
It seems, that AppleTV2 only plays Dolby-Digital, if this stream has the enabled-bit in its meta-data. In the files generated by the turbo.264hd, both streams (AC3 (=DolbyDigital) and AAC (=stereo)) are included, but only the AAC has the enabled-bit set.
I think, if encoding using Handbrake and you include both streams, then it works, if the AC3 is the first stream and the AAC is the second stream, because the ATV2 seems to use the first stream in the file, which has the enabled-bit set.
In the elgato-forum I got the hint to use a small program called "Subler". This program can demux a M4V-file. It also allows to change the meta-information in the file: you can disable the AAC-stream and enable the AC3-stream. this only changes the meta-information, but does not delete the AAC-stream, it will still be included. Subler does not need to reencode or remux the file, it just changes the meta-information and saves the changed video-file in less than one second! So it is ultra-fast. From now on, the ATV2 plays this files with DolbyDigital enabled 🙂
Please cross-check:
http://forums.elgato.com/viewtopic.php?f=128&t=9298
Regards
Florian