@TwoOfFive...
I've read a lot of your posts... can I just ask... why are you worried about WMP or Windows Media Centre? It's clear that you hate it.
Why not look at something like Kodi. You can install it with a clean Ubuntu install straight off a Live CD? No need for a pre-existing host OS (although you can run it under an existing install of Linux or Windows if you wanted to). It's far more customisable and works very well.
https://kodi.tv/
You know, Windows Media Center/Player is actually a pretty good piece of software, and I have to say it's the closest thing to good Microsoft had gotten to in a while. Right before they removed it from Windows and it died. I also don't have Ubuntu, I have Windows Server 2016, which is actually pretty good. It's lightweight and it drops most of the stupid things about Windows 10 like the desktop bloatware (replaced with server bloatware, but some of it is more useful than the desktop rubbish), Cortana is gone, forced updates are gone.
I also do not think it is the file as they have worked for years. It's also not a specific point that the video breaks down. It doesn't reach any specific time before it stops, it just stops at a random point, or if you do a few jumps to different times.
I will however try MKV2MP4 and see if VLC/WMP like the wrapper.
Oh, and another thing I don't like about VLC is the UI. The thing about Windows Media Player is I can have it playing windowed and it will look fine. All it has is the title bar and I don't have to deal with the stupidity of fullscreen, especially since I often change videos, and I watch my videos while working/playing games (Yes I play games and watch videos at the same time. XD) I know you can probably mod the VLC UI, but the WMP UI is actually pretty good. I think it actually looks better than VLC's very simplistic UI. I like the translucent menus and minimalist features. Of course VLC is like a swiss army knife. It plays everything and it can do everything. In the lack of WinX DVD ripper (Which rips EVERYTHING, but it will cost you everything) it is probably the best DVD ripper you can have. It can even play region locked DVDs on locked players (Something WMP always yells at you about when you even put the stupid thing in)
But I will try MKV2MP4 and come back with my results.