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The ATV is connected directly to my Home Cinema via optical out and performs perfectly for all other files I have converted using Handbrake. I can change settings and use a pseudo surround, but I would prefer the proper separate channels. This problem file converts and works perfectly with 6 channels when converted from MKV to m4v using Handbrake, but not when using Subler. The only other MKV file I have converted with Subler worked fine, so there must be something odd about this problem one.

I will see what happens on the next MKV I try to convert.... I'm not giving up on Subler yet ;-)
One of at the things Handbrake does is convert your 1st audio track to AAC stereo. The aTV looks for that track. I would suggest taking a look at the files you have that work and see if the 1st audio track is the same or different than 1st track your problem file.

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guys, keep in mind just because something is h.264 doesn't mean it's compatible. Apple tv (and probably other things like itunes) only support playback of certain h.264 profiles/levels. Chances are the h.264 video in your matroska container isn't a supported type (it rarely ever is in my experience).

This is why converting it via handbrake profiles always works; with the right profile, it will always produce a video stream that your device is capable of decoding.

If the h.264 stream in the container is not one of the supported profiles/levels, i'm afraid there is nothing else to do but convert it to one.

+1
 
Thank you 'mic j' for that very useful info.

I am starting to get a grip of this now so will try some more tinkering. The pesky MTV also has another audio track in a foreign language, so if I can get that to the top of the list it may convert that to stereo and keep the 6.1 English tract intact....
 
Guys, keep in mind just because something is H.264 doesn't mean it's compatible. Apple TV (and probably other things like iTunes) only support playback of certain H.264 profiles/levels. Chances are the H.264 video in your Matroska container ISN'T a supported type (it rarely ever is in my experience).

This is why converting it via Handbrake profiles always works; with the right profile, it will always produce a video stream that your device is capable of decoding.

If the H.264 stream in the container is not one of the supported profiles/levels, I'm afraid there is nothing else to do but convert it to one.

This is much less true than it used to be. Since the latest release of iTunes to support the iPad and ATV 3, they support 1080p, high profile level 4.1 (iPhone does as well). This is the highest level in general use (the one used for Blu-ray discs)

I find MP4 Tools a much simpler option than Subler (which just didn't work at ALL for me) or Handbrake.
 
Thank you 'mic j' for that very useful info.

I am starting to get a grip of this now so will try some more tinkering. The pesky MTV also has another audio track in a foreign language, so if I can get that to the top of the list it may convert that to stereo and keep the 6.1 English tract intact....

Here's a possible way to do get a stereo and DD5.1 audio tracks in your file using Subler without moving the other language track to the top (although that might work).
Set your Subler preferences to "convert AC3 to AAC" and select the audio format to be Dolby Prologic II.
Open a New file in Subler. "Add" the file you are interested in, checking only the tracks you really want (lets say video and AC3 5.1 audio tracks). Save.
Go back in to preference and uncheck the "convert" option.
"Add" the same original file but only check the AC3 audio track.
This should result in:
track 1 video
track 2 audio (AAC Dolby Prologic II)
track 3 audio (AC3 5.1)

This is a general outline that you will adopt to your specific file.

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This is much less true than it used to be. Since the latest release of iTunes to support the iPad and ATV 3, they support 1080p, high profile level 4.1 (iPhone does as well). This is the highest level in general use (the one used for Blu-ray discs)

I find MP4 Tools a much simpler option than Subler (which just didn't work at ALL for me) or Handbrake.

Agreed, MP4 Tools is a good alternative.
 
The ATV is connected directly to my Home Cinema via optical out and performs perfectly for all other files I have converted using Handbrake. I can change settings and use a pseudo surround, but I would prefer the proper separate channels. This problem file converts and works perfectly with 6 channels when converted from MKV to m4v using Handbrake, but not when using Subler. The only other MKV file I have converted with Subler worked fine, so there must be something odd about this problem one.

I will see what happens on the next MKV I try to convert.... I'm not giving up on Subler yet ;-)

I've remuxed thousands of .mkv to .mp4 files. Every single one has played back as expected on my ATV. Sometimes there are unusual formats or variations. Because you've indicated that the 6-channel audio from other converted files worked normally and the "problem" source file yields a proper audio stream, I suggest deleting the problematic audio from the remuxed file and muxing in the handbrake audio that does work. Just open the .m4v created by Subler, select the "bad" 6-channel track, delete it, then literally drop the Handbrake file into the Subler window, select only the 6-channel audio to import, click ok). By muxing in the working audio, you can preserve the video quality and have a working 6-channel audio track. Be sure to have only one audio track enabled and if you have multiple audio tracks (it appears there are english and hindi tracks) be sure to set them both to group 1.

Guys, keep in mind just because something is H.264 doesn't mean it's compatible. Apple TV (and probably other things like iTunes) only support playback of certain H.264 profiles/levels. Chances are the H.264 video in your Matroska container ISN'T a supported type (it rarely ever is in my experience).

This is why converting it via Handbrake profiles always works; with the right profile, it will always produce a video stream that your device is capable of decoding.

If the H.264 stream in the container is not one of the supported profiles/levels, I'm afraid there is nothing else to do but convert it to one.

You can force the profile to the ATV/iPhone compatible profile (Main 3.1) with Subler. Never caused a problem for me.
 
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