I do a similar process with my AJA I/O and capture via SDI with embedded audio. I believe that there is a limitation within Quicktime that only allows 2 audio channels at a time to be captured. Rumor was that this might change in the future, not sure where that stands right now. Four channel output is great though. I have to deliver Ch. 1 & 2 as Stereo Mix and Ch. 3 & 4 as Music and Effects. Hope this helps.