Well, I know it's a Gigabyte thing for sure, it's right in the manual and I've always had to disable it anytime I've used add-on audio cards.
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Of course, I'm no audio pro (Don't care), so maybe I've never tinkered with it the right way, and I've also only tried with one speaker source anyway?
For my speakers, I could only use one or the other, and HDMI audio via ATI was so tiny a gnat would squint to hear it. << And that may be the same issue the OP is having, I bought a cheap card to get around that, but have since went back to onboard. I only use speakers for mail notifications, or the occasional tech video, so it doesn't really matter to me how it's setup as long as it's working. I just dropped my thoughts here because it seemed like no one was mentioning this, and I had experienced similar with HDMI audio.