I have cable to the Tivo S3 and then an HDMI connecting to my Yamaha RX-v1700. I get constant audio dropout but only on certain channels (CBS/ABC).

CBS is the worst of the 2. I literally have to pause and play the Tivo to get the audio back. Usually it only happens when it goes to a commercial and comes back from commercial. It also sometimes drops and comes right back, like a hiccup.

Its not the HDMI cable since I switched that out already.

I'm not sure if you are asking a question or not.

Does the TIVO belong to your cable company? If so, perhaps swap it. Also sometimes the feeds are not perfect especially if the weather is bad somewhere.

It is a Tivo Series 3, not from the cable company.

I am asking why this might be happening and what I can do to fix it.

The sound literally mutes until I pause and play. OR, if I leave it long enough it will turn itself back on again at the next commercial break.

Well that is going to be very hard to say.

Do you have cable on other tv's? Do you have dropouts on those as well? If it is the Tivo, the cable company wont help you.

As I said I have dropouts on occasion with my Driect TV service.

i am wondering if there is some sort of a handshake issue going on between the tivo and the receiver.

Well you said you switched the hdmi cable, that didn't change anything?

You could try a different audio output and go straight to the tv for a test, that might yield something.

I have never had a SA Tivo, but I have had 3 different DirecTV versions. Sometimes things like this have come up for me. Have you searched/asked over at tivocommunity.com? Probably a good spot to look around. Usually it turns out some sort of reset or upgrading firmware (when a bad one came down the line) is the answer.