I'll try this again,
I'm ripping my Blu Rays with MakeMKV then I use MKVPropEdit to set the Track Names and Flags and MetaX to set Meta Data. After that I have a batch file that uses MediaInfo data to create a command line for MKVExtract to extract the Lossless audio for conversion to FLAC. During this extraction process I've discovered some odd behaviour from both MediaInfo and MKVExtract, at one point MediaInfo failed to detect a DTS-MA stream as DTS-MA so the extraction process failed, looking at the file with the MediaInfo GUI showed the Track to be simple DTS and it stayed that way until a re-ran the file through MKVPropEdit, afterward MediaInfo showed the track as DTS-MA and it extracted perfectly. This isn't MediaInfo related but at another point and ran the extractor batch, the command line built fine but MKVExtract extracted nothing. I just ignored these problems until I came across the file I currently have on my HDD. After running the file through MKVPropEdit and MetaX MediaInfo failed to see ANY tracks in the file at all despite the fact that it played perfectly in both VLC and Windows Media Player and MKVMerge could process the file fine. At that point I contacted the developer of MKVToolnix to discuss what might be going wrong, he created THIS FAQ for my benefit:
And told me the MKVExtract issue was probably being caused by me using MediaInfo Stream Order instead of MKVToolnix TrackID. So I ran the file through MKVMerge with the -I command and then used the MKVToolnix TrackID to try to extract a track from the file which MKVExtract failed to accomplish. I gave him a description of what happened and within hours, without even looking at my file he realised what was wrong, identified the bug in MKVExtract, fix it and gave me a link to the new version which I downloaded and used to extract the audio track. MKVExtract is fixed but I'm pretty sure it's not going to be that simple with MediaInfo. I have a 27.5 GB file on my HDD that MediaInfo insists has no tracks inside, I realise the insanity of trying to get that file to you but I'll try if you're willing. Other than that, since the problem is caused by the way the Header Editors choose to format what they write I have no way of recreating the problem in a smaller file as I have no direct control over the process. I've looked at the file in a HEX editor and am trying to understand what's inside but some of the formatting isn't intuitive and I can't find a good explanation for it, I'm waiting for the Matroska web site to reply to an email I sent asking for information. I could try to continue but first I should ask what you really need from me or if you even want to deal with the problem at all.