www.makemkv.com

I have the complete collection of FMA:B on Blu-ray. It rips fine, but when inspecting the file tree within MakeMKV before making the .mkv file, all of the Japanese audio is missing. Instead, there are two English tracks. When playing directly from the disc in the drive, the same situation occurs, but I can simply select the Japanese audio from the menu of the Blu-ray, which then turns one of the English tracks into the Japanese audio and renames it as such.
I have my preferred language set to none within MakeMKV.

However, the Japanese audio shows up completely fine in Handbrake so if I have to I can just use that if it comes to it, but I'd like to use MakeMKV for everything instead of jumping between software. If anyone has any insight, it'd be greatly appreciated!

One possibility that I have seen is that there are "two separate tracks" using the same data. One is English, the other is Japanese. Pulling either one gets you JUST the audio for that language, and you have extra work to put them together.

The DVD version of this title has all tracks in one "title"; it is possible that the Bluray separates them.

When I've had movies like this, I had to extract the English and Japanese versions separately, and merge them with mkvtoolnix later.