I am trying to do a similar setup. Mac mini HDMI out to Yamaha receiver (zone 1) Headphone jack out to Yamaha (zone 2). I also cannot get both outputs to work at the same time. It appears this is the answer.
Question: Do you have to do this every time you use itunes?
"then once JackOSX and itunes are running open the JackOSX routing window and direct channel one input to channels one and three output of the Aggregate Device and channel two input to channels two and four output of the Aggregate Device and it should produce correct audio on all four hardware output channels."
Thank you,
