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In November we switch from Direct TV to COX. Since then, we have on a consistent problem with audio sync issues. And it appears to be only in the main room. However the upstairs TVs are not used as often. We've had COX out multiple times. And it has not gotten better. Changed cable boxes, replaced the HDMI cable. Even the coaxial cable from the wall outlet to the box. Changed ports. And it is still happening.
However when using the blu-ray or streaming on Apple TV there is no sync problems.
What DVR do you have? I had similar issue. I was able to fix this problem under the audio menu on the DVR.