Okidoki, think i have something for you
The video stream is afaict H.264/AVC1/MPEG-4 Part 10 Main@L4.1 Profile (HDTV/Blu-ray/HD DVD compatible)
And my file has 2 audio tracks and some subs streams present (but not showing during playback, i can extract them though)
Atm automkv afaik with its internal/bundled filters/demuxers cant handle contained subs or avc1(high profiles) proper.
It shows fex, one audio stream though there are two.
If this is because the mkv container allows for custom stream info and thus feeds un precise info to automkv i dont know but seems plausible.
It did react much better to my remuxed mkv, i didnt let it finish but the output looked ok.
I also did get it to encode the H.264 stream only using ffmpegsource instead of directshowsource but it cant determine the fps or total playing time.
Automkv is unfortunately currently not very stable imo(and i havent bothered keeping track of good releases).
Fex. the auto deinterlacer check crashes too often, theres the preview/crop memory leak, hybrid interlacing is not well supported
and lately all my avi2avi encodes are horribly blocky and/or suffer from colour distortion and jitters(no matter the profile).
Keeping it updated is a hit and miss, and since most of its followers seem to be wmv, ipod or ps3 encoders, the main development focus is atm mainly on those parts and profiles.
So for now im using megui. Its getting close to a stable release and the latest build seems very good.
In fact i believe megui is superior in almost every way and the only reason ive used/recomended automkv is the easy setup and that it sometimes retains sync better that anything else i know of when doing certain "difficult" (dvd) sources, oh yes..and it does take movs and other strange animals which is definitely a pluss.
Heres my suggestion:
Get the latest matroska splitter
http://x264.nl/(megui too) and (i used)coreavc v1.5 (or later).
I believe H.264/avc1 demuxing and decoding also are supported in cyberlinks h.264 codec package, and propably some others too.
I stopped searching when i found something that works.
Other than that i used MediaPlayerClassic Home Cinema Edition(turning off the internal matroska splitter)
http://tibrium.neuf.fr/ and ac3 filter
If you still cant play the original mkv on the media pc, heres the remuxing and encoding steps:
To demux the streams:
MKVextractGUI
To remux the ac3 and the H.264 streams in a "clean" mkv:
MKVMergeGUI
Make sure you enter the appropriate fps for the video stream.
If you use mediainfo the original mkv fps will propably be reported differently than what youd get if you play the H.264 stream and look at its properties.
For megui to do the best job possible id go with the stream info not the mkv info
(if we have the same source mkv will show 25.00 and the stream will show 27.03)
This way all the streams info needed for megui to encode proper are in place.
Set megui to autoupdate from the development servers (settings | extra config) and let it update.
While youre in settings choose 2 passes in the automated encoding box, make sure the overwrite stats file in 2pass mode is checked,
and uncheck the "open preview after avisynth script selection" so the encode wont be slowed down by the preview.
Set codec to xvid and format to avi, the save path can be changed later or it will automaticly be set to the same place you save the avs.
Dont bother with the audio for now you can mux it when megui is done.
Start the avisynth script creator(tools menu), load the file, set source to progressive(or do an analyze, i do believe your source is progressive though), make sure its not resizing(resizing is always activated by default) and save the avs.
Make sure the desired profile is chosen in the video profile dropdown menu.
Start the bitrate calc(tools menu), input what you want and close. Its important because the bitrate from the calc will be automaticly loaded in the video profile.
Enqueue and encode. You will propably get a worker thread q, let it make one for you and it should be good to go
Remux the encoded avi with the ac3 and your done.
I did a full encode with the above filters and steps, came out beautifully.
Megui also has some muxers/demuxers in the tools menu, but the one ive mentioned i know for sure works so id stick with them for now.
Nothing wrong with experimenting though.
Of course you can try the remuxed mkv in automkv instead of megui,
As alwyas with different systems and configurations your milage may vary in either directions
Ill pm you with some megui profiles, and some other info.
And... as always
dont hesitate to ask if you want some assistance with megui or anything else!