Hello. I had a similar problem and wanted to share it in further detail along with a fix.
Background - I currently use an AppleTV (v6.0.2) which I run through my Denon AVR-1709 AV surround receiver (came with the house - I am guessing its approximately 5 years old). Since my receiver's Zone 2 (patio speakers) will not broadcast digital sound, I have been forced to use a digital to analog converter on the ATV in order to convert the optical cable coming from the ATV to analog. If I didn't do this, I could get rid of the converter and plug directly into the Optical input on the Denon - but then I would only get sound in Zone 1. (I don't understand why Zone 2 will not accept digital audio - but it specifically states that in the manual. I have a similar problem with a brand new Onkyo in another part of the house - problem for another day). Video from the ATV is hooked up directly to the Denon HDMI input.
Problem - When I watch Breaking Bad on Netflix via my ATV, almost all of the episodes broadcast static audio. I noticed that this problem appears to only happen on Netflix content broadcasting in Dolby Digital (with the DD logo). Older content (Magnum PI) and newer content not broadcasting in DD (Olympus has Fallen) does not have this problem. Problem is not limited to Breaking Bad (i.e. all other DD broadcasts have same problem).
Observations:
1. If I removed the Digital Analog converter and plugged the ATV directly into the Opticial input on the Denon - the problem was solved. But, as noted above - this doesn't help me because then I won't be able to get any sound to Zone 2 (i.e. can't play any of my music from ATV on those speakers).
2. I also switched the analog input from the converter into another analog port on the Denon and had the same static problem.
3. #2 led me to believe that my converter is broken or is at least contributing to the problem. But then I tried the link noted above (http://support.apple.com/kb/TS3518.). I went through all the steps and when I switched: (a) Dolby Digital to "off" and (b) Audio Output to "16 bit" - the problem was solved - all Netflix content broadcasting in DD is now working fine. The switch doesn't appear to have negatively impacted anything else (i.e. music still broadcasts, older netflix content broadcasts, etc.). So, until I discover a downside to this "fix" - I am going to stick with it.