Are you using the ducking feature? The ducking feature mutes all other clips except this one. If you want to mute the current clip, you click mute or move the volume slider.
See this Tutorial http://www.apple.com/findouthow/movies/imovie08.html#audioclips
I had a song playing through the whole movie and was dropping the audio to zero on the movie clips. For some reason it worked with every clip other than this one.
I've managed to solve the problem, but not quite sure how. I exported the movie from Aperture to become a referenced master file, which I then dragged to my desktop. I then dragged that file back into iMovie and for some reason it then worked - despite having removed the video and dropping it in afresh before.
No idea what caused it, but it seems to be working now.