www.makemkv.com

Several. Most recent examples: The Dark Knight, Blade Runner (Final Cut), Matrix 1-3.

Thanks, but the multiple copies are the same file size, same number of chapters etc. I'm wondering if they are just different directory structures leading to the same source file?

The mystery is why they output different size MKVs.

I've noticed on many Blu-ray discs there are often two or more copies of the main feature. While the original files are the same size they yield different MKV sizes. What gives?