The problem with using makemkv is after your rip it you have to then demux it so you can throw the video in handbrake. Kind of a pain. Just rip with eac3to. Throw the video in handbrake and then merge with mkvmerge.
I have been having problems with ripbot and quality lately. So I started using handbrake and I had the same errors as you. The fix is to use the snapshot build.
But I get better results with handbrake now. Settings are auto crop, high profile and save as an mkv. For the file size I get better image quality in handbrake.
Streaming Devices: Nvidia Shield TV, 2x Roku 3's, 1st and 2nd gen chromecast, Amazon Fire TV stick 2nd gen, Apple TV 4, xbox 360, xbox one
Displays: Vizio M602i-B3, LG OLED65B6, panasonic ax100u on a 145" S-I-L-V-E-R painted screen, 40" Samsung(don't recall model #)
Receivers: Denon X3300, Yamaha RX-V663. Bluray/UHD player: Oppo UDP-203
Retired - HTPC: Intel e6300 2.8ghz, Intel DG45ID, 2gb DDR2, Radeon 5570, MCE IR receiver