Minor detail, but it's a bit confusing that most apps (like VLC, WMP) start with title #1, but in the logs MakeMKV seems to start with title #0. I was processing Castle S01D01, and it did an awesome job of finding the 4 valid titles out of 99 on the DVD, but they were 1 lower than I had already determined with VLC Media Player.
Other than that, it appears to have worked great. Awesome application!