Hi Bob.
I have all my audio monitoring via Aja in to a Mackie mixer.
So everything that goes out from the Mac, Final cut, After effects, Pro tools, Itunes or what ever goes through the Aja card.
Now I also have a problem with the audio synch when I jump between different apps. The only solution is to restart Final Cut.
Worth mentioning is that this is a brand new editing station.
I have just switched from a G5 Power PC with a Decklink SD card to
a Mac Pro with Aja Kona 3.