Well, what's odd is when I rip them with MakeMKV - as Collector said, it's a container file, keeps all the chapters, etc - and also makes it like a 30GB file when it rips from BluRay.
When I then take Handbrake, and run it through there, it reduces it to like 5 to 10GB files (depending).
And when I tried to just rip with Handbrake - it rips EVERYTHING (maybe there's a way to change this, I don't know), where as MakeMKV allows me to select what I want to rip.
So all the files always work as MKV files. It's when they run through Handbrake, one out of 100 suddenly only plays audio with WMP, but plays correctly with VLC.
So I'd think that rules out the ripper - since it works as MKV files. It's something, that from time to time, Handbrake is not ripping the right codec. And it can't be based off the DVDs, because like I said - it can be a DVD with 4 episodes of say, Veronica Mars. All rip fine as MKVs. However, when I run them through Handbrake, one out of the three, might just only play audio with WMP (and work with VLC). You'd think the same DVD (that has all four episodes on it), would have the same codec.
Regardless - I found a way around it. I just play it with VLC (the few that don't work with WMP), and capture it with Fraps - then run that capture through Handbrake, and it works.
Bit of a pain, but it happens so rarely, that it's not a huge burden.