i have same problem. The New Apple TV has messed up my hdmi-cec. When i pulled apple tv of the box it was controlling the tv power and volume. Now even after being powered on/off several times, it won't control tv or volume (even though its set to On to control it) and I now can't control the TV's volume from its own volume control more, i have to use the AV system's volume. Even if it turn hdmi control OFF, my tv remote won't control AV system anymore. Using old apple tv I was able to control tv volume from tv's remote, now even that doesn't work. Also I've had difficulty flipping from Xbox to Apple tv, (never had that issue before) , sometimes shows black screen instead apple tv, sometimes it shows several green screens then apple comes up. Also i have switched backgrounds from Aerial to Photostream -- several times, it wont' save it. it says its there, but then goes back to Aerial every time.
For reference i have a Sony Bravia.