You may need to de-multiplex or "demux" the audio from the video. Some AV formats (mpeg) combine the audio and video information into a single stream, whereas others don't (DV). To work with the info separately (read: at all, wrt the audio portion) in FC, you need a program that can unmix the info.
A pretty good one is MPEG Streamclip. It's small, quick enough for minor stuff, and while I can't vouch for high-quality output, I had no problems with it. Further, it's free.
When you get the output file (raw DV, I expect), try that -- should be fine.