www.makemkv.com

I solved my problems. I found various errors in /var/log/kern.log all related to the sata interface my optical drive is on. I swapped out the sata cable to that drive and the problems went away. So it was either the cable or a loose connection in my case.

Also seeing this problem on Debian Jessie.

MakeMKV v1.8.12 linux(x64-release) started
Using direct disc access mode
Evaluation version, evaluation period expired 12 day(s) ago
File 00801.mpls was added as title #0
Title #00007.mpls has length of 14 seconds which is less than minimum title length ...