OK, you have the opposite of my habit. I rip the individual titles, and skip the combined. Your error reports are at the point where the tracks are patched together to make the bigger track, and Funimation doesn't always do those "right".
The seven tracks you have unchecked are the individual episodes (5 chapters each), and the checked one is "all of the above". The contents are the same, but the transition from one to the next can be very good (like the first couple of disks), or horrid (the ones you're having issues with). The reason the Japanese flows smoothly is that the original tracks were Japanese (they're also in LPCM, a different encoding method), and Funimation stuffed the English (DTS-HD MA encoding) in on top of that.
In this case, your choice is really which audio is important. I'd do it the way I did it, of course.
![Rolling Eyes :roll:](./images/smilies/icon_rolleyes.gif)