I know that atres names hulu downloads as mp4 when the container is actually flv, and a slightly strange flv container that FLVExtractCL won't recognize.
You may want to check the container on the atres download. Simply copying the contents may fix the duration.
Code:
ffmpeg -i "atres_download_name.mp4" -vcodec copy -acodec copy "new.mp4"
If you get any errors about the aac track, then the aac_adtstoasc step might not have been done when/after atres downloaded the file.
I found the 6902579_1280x720 entry. I overlooked it the first time thinking it was the same 720p entry as the other one in the playlist.