I am currently ripping my entire BR and DVD collection to mkv using makeMKV. I've ripped about 40 BR discs so far and have not encountered any issues, apart from Apocalypto. The movie stutters and loses frames in many scenes and it does not matter what player or computer I use.
The original BR plays perfectly fine on a computer or BR player.
Any ideas?
Edit: I've been doing some searching and it looks as though I am not the only one having issues ripping this particular disc. People are reporting issues when using various rippers as well.