I bet it’s a coincidence and related to something else that’s the same for those 39 movies.
The command for extracting VP thumbs ignores audio completely, so I’m guessing it’s not the FLAC. Obviously it uses the Plex Media Transcoder
but it’s something like this:
ffmpeg -skip_frame:v nokey -i input.mkv -q 3 -filter_complex "[0:V:0] fps=fps=0.500000:round=up,scale=w=320:h=240:force_original_aspect_ratio=decrease [out]" -map "[out]" img-%06d.jpg
You could run that manually and see what happens. You’ll get a lot of .jpg files if it’s successful.
Did you see the other threads about index-sd.bif generation failures? There are some workarounds you can try.
FFmpeg is a bit inconsistent about what it calls a keyframe. That means the -skip_frame:v nokey
option Plex uses can cause FFmpeg to fail to extract preview thumbs on some media.