I checked out your logs, it appears that’s some issue with the original video:
2019-09-05T18:35:09 MCEBuddy.AppWrapper.FFmpeg → [mpeg2video @ 0000000002a72940] Invalid frame dimensions 0x0.
2019-09-05T18:35:09 MCEBuddy.AppWrapper.FFmpeg → Last message repeated 4 times
2019-09-05T18:35:09 MCEBuddy.AppWrapper.FFmpeg → [mpegts @ 0000000002a71000] PES packet size mismatch
2019-09-05T18:35:09 MCEBuddy.AppWrapper.FFmpeg → Last message repeated 4 times
Whether it’s minor or major I can’t say. The only difference between comskip and showanalyzer is that they have different detection algorithms, so the commercial marker points would differ. It’s possible that the marker points selected by Comskip have some video data corruption at those points in the original video may be causing the issue. Have you tried playing back the converted file in VLC? Sometimes it’s the player codec which has issues.
The only way to tell would be to look at the original and converted videos. If you upload them to the MCEBuddy server I can check them out.