Well, first of all, why are you changing from 720×486 to 720×480? If you want the 720×480 frame size, you should work in DV and not uncompressed 8 Bit. That might be one of your problems, don’t know why this would happen, but maybe.
Next, if you are in FCP5 click on the clip settings tab of the log & capture window and make sure the tickbox for both video and audio are selected and that the proper channels are turned on for your audio settings (channels 1&2, dual mono, stereo, whatever you want).
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G5 Dual 2Ghz <> 4GB RAM <> FCP 5.02 <> Kona 2
ATTO 42XS <> Huge Systems 4105 Fibre