With my 290 for whatever reason it only seems to encode properly if I don't have my monitor hooked up to my receiver. I'm assuming it's a thing with HDMI 1.4 vs 2.0 (my receiver does 2.0 but my card doesn't yet, so I can't really investigate.) Or possibly an issue with the drivers/TrueAudio support that doesn't show up in normal usage, but I haven't been bothered enough to ask AMD about it.
My consoles are also hooked up to the receiver so I'm usually just going back to the original 5.1 setting.
And now I'm no longer primarily a PC gamer. *shrug*