MakeMKV or any other tool aimed to create an .mkv file from an optical disc are not supposed to generate the exact same file every time.
Like ndjamena said, .mkv files have some extra information to the video/audio/subtitle. Let's just observe the file I just created with MakeMKV with ffmpeg.
Code: Select all
Input #0, matroska,webm, from 'title00.mkv':
Metadata:
encoder : libmakemkv v1.9.8 (1.3.3/1.4.4) x86_64-unknown-linux-gnu
creation_time : 2016-01-20 02:08:52
Did you notice the version number and the creation time? Yes, that's the reason every time you create an archive with MakeMKV, the checksum varies.
If you want a precise dump of your disc, without anything appended, you should consider a disc-level archive, which means you dump your disc with tools like UltraISO/IsoBuster/CloneCD and output as bin/cue. Search the Internet for more information.