In some cases, it's not possible to record audio using Soundflower (that's what is used when you check the "record computer audio" option in iShowU HD).
- The application doesn't support it (RealPlayer)
- You're using Logic, or ProTools - and don't want to (or can't in the case of ProTools) change the project so it sends its output to the Soundflower 2ch device.
Solution - Use a cable
A way around this is to use a cable to route the audio back into the mac, and record it as though it were a microphone. This requires of course that you are playing your audio mix back to an outboard audio device, such as a mbox.
- Make an audio connection from the mixer back to the Mac. This could be a SPDIF or 3.5mm Jack > headphone type connection. Either way, you want to get the output of the entire mix back into the Mac.
- Have iShowU HD record that device. SPDIF or Built-in Line In, depending on the type of physical connection you make.
This method has the advantage that a you don't have to muck about with project settings to get the app to play sound to the Soundflower device and b It also means you get to use the mixer as ... a mixer, and can adjust your mix accordingly and record the final output.