Manual video preset function does not initiate full transcode job with FFmpeg

I have determined that the video_presets module does more harm than good for the purpose of transcoding with FFmpeg. So by eliminating that completely, building a site without it and creating presets minimally, I can see that transcoding jobs are failing for a variety of reasons. This function may be the key reason why I cannot get this module to work with FFmpeg.

I have a working copy of FFmpeg that I built myself in order to produce mp4, webm and ogv file types, as well as to decode Apple ProRes 422 and 4444 files. I know it works because I can run transcoding jobs from the command line. Unfortunately, the video module does not apparently send useful commands to FFmpeg, nor does it pass back the results of the transcoding jobs that are run unless one transcodes using cron and "drush cron" is run in a shell, which produces the feedback.

One thing I have noticed is that changing the Video preset in /admin/config/media/video/presets/preset/(extension) from "none" to anything else like "libx264-baseline" kills the transcoding job. Nothing happens at all. (I'm also not sure why this list of options would exist for other presets with different codecs.)

Another thing is that when the Video preset in /admin/config/media/video/presets/preset/(extension) is left at its default of "none", a small file is created with the chosen extension, but no content is created. The contents of the file is strangely just this:

ftypisomisomiso2avc1mp41freemdat

In case it helps, here are some of my notes for reference. They outline my process as a sequence of node creation.
http://video5.mkdev.org/