This weekend I reconfigured my setup and removed my Onkyo rc430 from the middle of the HDMI configuration. I've had issues getting the audio sync right since I got the set, and suspected the Onkyo may be at the heart of it. So now the components go direct to TV with HDMI and then loop audio back to the receiver via toslink.
I still need to move my Uverse DVR over, but so far it seems the audio is better with both my 360 and Bluray player. Not sure its perfect, but the perception of it being off is diminished. I'll know better when I move the final component and test some more.
I know that some of the original audio issues were with my "new" setup, but I wonder if those that are having lingering problems are passing through the receiver with HDMI, There are some downsides for sure (no onscreen configuration for receiver, needing to mute tv when I want to use receiver) , but also upsides of having not having to turn game mode on and off with the xbox.
One last note, I adjusted the ambient light sensor down to medium, and the flashlighting I had in the left corner is now barely noticeable. It was really bothering me before. I have a few more tests to do, but am now optimistic I'll be able to hold on to this set.