It might be multiplexed, or muxed, audio -- the audio's encoded within the video track. AE needs a separate audio track. I recommend transcoding the clip to a good intermediate codec to separate the audio from the video and preserve image quality.
Oh boy. That is alot of clips to deal with unfortunately! Gotta be another way?
Do a short test clip -- if it works, you know the problem.
Take heart-- Adobe Media Encoder will do batch transcodes. You won't have to do each clip individually.