Zed,
Are you sure that audio in the FC movies is aiff? I think that .aiff and .wav are just two ways to envelope the same basic signal that is a PCM (pulse code modulation) that is the kind of audio that you get in the FC movies. If you open the setting of a sequence, you do not see aiff nowhere, and If you export a .mov and you open it in QT and them you open the info window, in FORMAT you will read: 16 bits integrer….but nothing about wav or aiff. these formats you get them when you export audio alone.
Cheers,
rafael