Just a word for anyone that's muxing this together with the movie file - the commentary should be played 2 seconds early to really line up properly with the movie. If you're using MKVToolnix GUI, for example, you'd want to set the delay to -2000ms. (This was using the FLAC file, I didn't test the MP3 but I assume it's timed the same)

I'd also recommend NOT using the FLAC file directly if you're muxing them together, unless you plan on only playing the file on a computer; most set-top hardware can't deal with embedded FLAC files. I re-encoded it to AAC to match the movie's audio track after I realized my Blu-Ray player couldn't read the FLAC, but the encoder doesn't really matter much for a commentary track as long as it's compatible with your hardware; you might as well go with the MP3 and save yourself the trouble, it should work with just about anything that can play the movie file.

Thanks for the info! I muxed the commentary into the video file (with your recommended delay) as soon as I downloaded them, but I didn't watch the movie until a few months later. I was holding off on replying to this until I watched it and listened to the commentary to confirm.

-2000ms on the audio did make the commentary match up exactly at some points. However, there were other parts that the commentary where it seemed to stray one way or the other. It seemed like they recorded it in sessions/sections, then merged them all together at the end, making some parts too early and some parts too late. -2000ms seemed to be the best middle-ground though, so I would agree with your recommendation of that amount of (negative) audio delay.

As a side note, I used the MP3 file for the commentary, so it does have the same issue as the FLAC (as you assumed).