There's a place in the settings to choose the source. First make sure that the 1/8" minijack cable from the video card (the one bundled with the video out cables) is going into the line in on the soundcard, then make sure that the line in is chosen in the ATI settings to be the audio source. It might also help to check if line in is the recording source in Windows. I'm not sure if the ATI software cares about that, but it's worth a shot.
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Matt