I've seen others complaining about this since launch - it still hasn't been addressed. Using the Google TV in 5.1 mode causes a sync lag between the audio and video by a few frames. It's not terribly obvious, but I can't ignore it and pretty much don't use my Google TV anymore because of this issue.
Google - PLEASE fix this.
I have the same problem. It's not on all apps or all stations. About the time I think it is better it comes back. So annoying. Google support forum has a post from October that has an acknowledgement from December and still no fix with hundreds of complaints over 9 months.