There is a slight difference between original encoded MP3s and the ones extracted from other formats and most common issue is related to how the MP3 is extracted and what are its headers.
I recommend you to re-extract the file, but this time use another application and use other settings as well.
You can use the Media.IO software to to this: http://media.io/
Additionally, extract the audio stream from MP4 to WAV, since WAV has better support.