One thing you might try if you have another audio recording/editing program (protools, logic)… try playing back the file and capture it in the audio program, then make an aiff or mp3 and bring in the files separately (mov conversion and aiff or mp3) and re-align in final cut.
I also use the conversion tool Procoder…for some reason it seems to split out the two tracks (unlike compressor or cleaner) and make a quicktime movie that imports fine.