www.makemkv.com

I have ripped Star Trek: The Original Series Remastered season 1. It contains commentary in 3 formats that complement each other and are all turned on or off at once - subtitle-based, audio-based and video-based (to go along with the audio, played in a picture-in-picture box in the bottom corner). The subtitle-based commentary, and probably the audio-based commentary (though that's DTS Express which mplayer won't read so I can't test the latter), have ripped fine, but the video commentary (that plays in a Picture In Picture-style thing) is nowhere in sight. For reference, I'm ripping the European version of disc 1, on which the Starfleet Access episode is Where No Man Has Gone Before. I have set the minimum timing to 0 seconds, and ripped every available file, and it is definitely not there.

If you need any additional information, I'd be happy to provide it.

MakeMKV currently ignores secondary video streams (PIP video). Technically, it's quite possible to put this video into MKV container, but pretty much no player would display it properly.

Fair enough, then.