Your original MKV files has lots of errors in it which is causing the issue.
2018-02-11T21:18:58 MCEBuddy.AppWrapper.FFmpeg → [aac @ 0000016cc25dd0e0] Sample rate index in program config element does not match the sample rate index configured by the container.
2018-02-11T21:18:58 MCEBuddy.AppWrapper.FFmpeg → [mpegts @ 0000016cc25daf60] decoding for stream 1 failed
2018-02-11T21:18:59 MCEBuddy.AppWrapper.FFmpeg → [mpegts @ 0000016cc25daf60] Could not find codec parameters for stream 1 (Audio: aac (LC) ([15][0][0][0] / 0x000F), 0 channels, fltp, 321 kb/s): unspecified sample rate
Did you record this on Emby? If so check out this post, you need to disable a setting:
The other option would to try to check the option for “Skip remuxing” in the Expert Settings of the Conversion Task. That may solve the issue because it’ll skip a few steps, however the long term solution would be to find out why your recording is the creating non compliant video