I don't know if this is any help or not, but I have been learning my way through converting a lot of Blu-Ray, DVD and other forms of video over the mp4 & MKV's for use on Plex with handbrake and for use on my Roku's.
An I don't know why, but it seems that even when I put several audio tracks on there, they can not be switched even if I do them in Plex/Web as the only thing that will play is what ever is the first audio track.
I'll admit I haven't persured it deap in the settings where I'm messing with the transcodeing choices, kinda thought I was setting things up to not need any transcoding by doing them in handbrake like many recommend. As well am running myPlex off a pretty cheap laptop with 3T USB drive on it, so I am trying to have as little need for transcoding as possble.
But at any rate, basically I'm writing this to tell you that for me I have learned that if there is a certain audio track I want from the various ones something might have that I am converting, I make sure I put it first.
So don't know if that will help you, kinda looks like your putting the 6 ch's first but perhaps those are ones that have that?
Anyway, know it might be a pain, but if you could do this you might try redoing them with checking to be sure which ever track isn't a problem an plays right is used for the first one, and reconverting it with that first.
Btw some of the ways I have been testing my conversions first for all kinds of things is to do a test run of say 120 seconds or something, then put that file in what ever myPlex folder I am going to be using it in first, then see how that works.
Then if all is OK, then I let the many hour conversion run.
Hope that is if some help