www.makemkv.com

I have English set as my preferred language, so I don't have to manually remove all the foreign-language subtitle and dub tracks that come with most major studio releases.

However, this sets the first English track as the default track and moves it to the first audio track, regardless of where it is in the original. Thus, if I'm ripping a foreign-language film with an English audio commentary, audio track 1 is the commentary and audio track 2 is the actual film audio.

Is there a way to stop it doing this without having it also select every track by default?

Not through the menus. You can establish audio selection criteria (there's a message about that in the Advanced Usage forum), but it doesn't cover all possibilities. MakeMKV favors "higher spec tracks", and sometimes the commentary tracks have more channels than the movie tracks.

Since I post-process everything with handbrake, I just have MakeMKV extract all language tracks, and make changes when I have handbrake process things.