Not a bid deal, but the chapters seem to be randomly chosen and not mirrored to the official dvd/blu-ray as they were on 2.0. Hopefully this will be changed on the blu-ray release.
EDIT: Just noticed the 2.0 AVCHD has the same chapters as 2.1, however the mkv of 2.0 had better placed chapters - odd.
EDIT 2: I know I've said it before, but just wanted to say thanks again to Harmy!