Sure.
Download Remux from here :http://www.macupdate.com/app/mac/35968/remux/
Then, drag and drop the original mkv into the program.
Under the "Reencode" column in the same row as the audio, it should default to "no". Click the scroll down menu and change to AC3 448k.
Set an alternate save location (or rename the file) or else your original file will be overwritten and the conversion will fail.
After Remux does its thing, you will now have an mkv with a AC3 audio track rather than DTS.
Now, drag and drop this new file into Subler. Passthru both the audio and video track. Rename this audio track "Surround Sound" or something like that.
Then, drag and drop the same file into Subler again, this time only keep the audio track checked and use the drop down menu to select "AAC - Stereo". This will convert the AC3 track to Stereo audio for playability on an iPhone/iPad. Rename this track "Stereo" or something similar.
If you want to save the original DTS track as well, just repeat the step above using the original, unconverted mkv, only check audio, passthru, and rename to "DTS" or something similar.
You should now have a video track and a couple of audio tracks in the Subler window. You must order them as follows:
Video Track
Stereo
Surround
(DTS)
Or else the resulting mp4 will not play audio in iTunes.
Now use the magnifying glass in the top right corner of Subler to add metadata, etc.
Then, click the video track and a few options should become available to you. Make sure the video profile is set to main@3.1 (I've heard the aTV can support other versions, but its not officially listed on the Apple site, so main@3.1 is what I use).
Then, when none of the tracks (video, audio, etc) are highlighted, an "Other Settings" menu becomes available. Use this to set the file as 720p, 1080p, etc.
Finally, when you are ready to go and start the process, if your file will be >4GB, you must check the "64 bits chunk offset" option in the "Save As" menu.
Hope this helps.
OK, I downloaded a MKV sample of 1:26 with tons of audios in both DTS and AC3. I took out with MKVToolnix the most of them and left DTS: SPA, DTS: ENG, AC3: ENG.
My plan was to convert this to M4V using Subler, see if the DTS tracks had acquired any kind of delay but not the AC3 one and then use remux to convert the tracks to AAC and then use Subler to put it to a M4V container and see if it had fixed the delay.
Problem is Subler did just fine. No delay. So... Only things I can think of are:
1. Syncing problem shows up with large files.
2. This is completely random.
3. Remuxing with MKVToolnix kind of solves any possible syncing problems Subler provokes.
Will have to try with a larger file, but I didn't have that much time so decided to do it tomorrow. It'd be funny now that Subler showed no delay at all with any of the rest of my movies. LOL