Ah, so to make sure I understand, are you saying that the logs are saying the subtitles are not embedded, but they actually are in the resulting file? I can open First\NFL Football - S2019E2069 - Kansas City Chiefs at Detroit Lions.m4v in either Handbrake or VLC and see the subtitles embedded there as a result of the first conversion task. Again, the log file for this task contains the same error code found in that log file as with Second that you mentioned earlier.
Unfortunately, I do not have another machine/environment readily available to try this out on so will have to see if I can get it working with the current configuration if at all possible.