Surround Sound drops in/out on some channels

I have had a problem with surround sound ever since I upgraded to a receiver that could output it. I'm using an HDDVR (according to info is an HR23/700). I've seen some other posts where people have similar problems. I'm outputting the surround over optical, with video over HDMI. Some channels are fine, movies from HDNET movies or pay per view are fine, but shows on Comedy Central like Futurama usually lose sound for about 3-4 seconds, anywhere from 2-5 times per episode, often during the punchline of a joke! The Dolby Digital indicator on my Onkyo receiver goes away while the sound is out, then comes back. It is probably a short blip in the signal and the silence is several seconds because my receiver is changing out of/into surround mode. My signal is fine, my HD picture is fine. I think it has to do with the broadcast, not my box talking to my receiver, because it is fine on some channels, and when I rewind or watch a DVR'd episode, the sound drops out in the same place every time I play it, so it isn't a random error in my hardware, it is something in the broadcast signal. If I play it back in stereo it is fine, but I didn't set up a nice home theater for stereo and simulated surround. I just haven't had decent surround yet and it is part of what I'm paying for, so has anyone found a solution? Will DirecTV replace my box with one that doesn't have the problem if it can't be fixed? Thanks for any help you guys can offer.