Seeing as MP3Tag is the only tagging app I've found that recognizes nearly all the categories of metadata in an MKV file type, (I've tried using MKVToolNix and can't find, say the "comments" section).. I've noticed that sometimes the app doesn't recognize every MKV file, even when the files are all created by the same encoding app, like MKVMerge.
I like using the comments section in metadata because with Explorer it's easier to separate TV shows by the season.. S1, S2 etc. Now, some of my files reach near the 15 to 20GB file size mark, and re-encoding takes some serious firepower.. so, what am I missing to help the app recognize the missing file?
If a screen shot is needed, or info from the app... please let me know, or if I'm not clarifying clearly.
I've tried to look thru each line of available metadata to see if there was something the encoder missed, but MKVToolNix doesn't show half of what MP3Tag can.. and it's more detailed in areas I don't really need.
I can try to re-encode it to another MKV container (I did this to MP4, but nearly doubled the bit rate and file size), maybe like you mentioned, something went wrong in the mass of 1's n 0's that just aren't visible to you and I, but are to MP3Tag.