Final Cut Pro or Compressor Audio Issues

I have been sending .mov videos that I post lectures for my college on Vimeo to Compressor from Final Cut Pro, but recently a lot of the videos I've been compressing have been appearing with no audio. Actually, that isn't entirely true. The music in the intro to the video has audio, but when the professor starts speaking the audio is silent. I wasn't sure if this was a Final Cut issue or a compressor issue. In order to "fix" it we've been exporting the videos as a master file and then sending it to Compressor, which works, it just takes a little extra time.

If anyone can help me figure out what's going on or can help fix the problem it would be much appreciated.

Thanks!