The difference is PCI vs PCIe in the chipset (then the data is routed via QPI to the CPU). The internal audio is attached to the PCI links in the chipset, as is USB and FW (Audio ->USB via the chip used is also possible).I don't see how that works, as onboard speaker does it, optical out does it, analog out does it and any FW/USB attached output does it.
Whats so special about the PCi-E sound card? :/
As we get into this, its beginning to seem like the Core Audio is the culprit, in how it interacts with the new chipset for the LGA1366 CPU's.