I'll post a new answer, rather than edit other answer, as my first answer is already rather long.
First, I would try to get to the bottom of the problem by starting simple and working my way up on the problematic file/s.
Just copy source to destination:
ffmpeg -i source.mp4 -c copy destination_1.mp4
Is the ouptut as expected? Any errors? What did FFMPEG display?
Copy video - encode audio:
ffmpeg -i source.mp4 -c:v copy -c:a libfdk_aac -ac 2 -ab 128k destination_2.mp4
Is the ouptut as expected? Any errors? What did FFMPEG display?
Encode video (simple) - encode audio:
ffmpeg -i source.mp4 -c:v libx264 -b:v 4000k -maxrate 4000k -bufsize 4000k -c:a libfdk_aac -ac 2 -ab 128k destination_3.mp4
Is the ouptut as expected? Any errors? What did FFMPEG display?
Encode video (+opts) - encode audio:
ffmpeg -i source.mp4 -c:v libx264 -x264opts keyint=24:min-keyint=24:no-scenecut -b:v 4000k -maxrate 4000k -bufsize 4000k -c:a libfdk_aac -ac 2 -ab 128k destination_4.mp4
Is the ouptut as expected? Any errors? What did FFMPEG display?
Encode video (+filter) - encode audio:
ffmpeg -i source.mp4 -c:v libx264 -x264opts keyint=24:min-keyint=24:no-scenecut -b:v 4000k -maxrate 4000k -bufsize 4000k -filter:v "scale=1920:-2" -c:a libfdk_aac -ac 2 -ab 128k destination_5.mp4
Is the ouptut as expected? Any errors? What did FFMPEG display?
If you still get problems it's going to be difficult to fix or make further suggestions without us seeing the output from FFMPEG.
Remember, don't use -crf 18 -b:v 4000k
in the same command, one or the other, cfr
OR bitrate
, not both.
Best of luck...