This is noted on many forums. DBSTalk
According to the support threads on DirecTV I have read (can't find it because it's buried b/c people keep posting their exact same issue there as if it is new), this has nothing to do with line of sight.
I think that by FAR the best evidence for indicating that this is not a line-of-sight issue is that my brother (and many others) has this issue on the mpeg4 channels on U-Verse. His TV accepts DD (he has no speakers) - and even his TV audio would cut out. He reported to me that some channels would cut out every 10 seconds - making them unwatchable.
When I tested this with my OTA locals, I can record both the OTA uncorrupted signal and the DirecTV mpeg4 version. The OTA version has no dropouts. To me, this points pretty clearly to the encoding that occurs to transfer the signal to mpeg4 - vs. the mpeg2 currently being used locally for OTA broadcasts.
Also, as DirecTV has moved more channels over to mpeg4, I have noticed more dropouts.
The explanation I am inclined to believe right now is that this is an issue with mpeg4-encoded material that uses the AC3 audio codec. The audio codec "skips", and the sound drops out.
You can switch from Dolby Digital to "Off" on your DirecTV receiver - and you will find that these dropouts practically disappear (they are still there but drastically reduced so as to be almost inaudible - I doubt I would have noticed them at all had I not known where to look). My brother is using this solution on his U-Verse - and his dropouts have practically disappeared when I last talked to him. Of course, his setting is not "Off" - I think it was "Stereo" on his STB. I just talked him through it last week. At first he thought it was the new TV and was talking about returning it!!
As you stated, you can easily rewind a program to the spot of the audio codec hiccup and reproduce it. When you find a dropout, try turning off Dolby Digital on your DirecTV box and then rewind and see if you can still tell the dropout is there. If I watch and listen very, very closely, I can still detect the slight blip even with DD turned off.
If you prefer to use this "solution", you can use Dolby PLIIx (or whatever) to recreate the surround sound. I have chosen not to do this and suffer the intermittent dropouts, because I find the fake version to be lacking compared to the actual Dolby Digital, and my dropouts are usually very intermittent (although some shows/channels are better than others).
My guess is that these minute audio signal dropouts are exaggerated on most modern HDMI receivers due to the decoding that is required in Dolby Digital setups, and so most people with these receivers are using Dolby Digital and a real sound system. That might explain why many people tend to point to certain "brands" of receivers as the culprit for these issues - and then proceed to list nearly every popular consumer brand AVR (Denon, Onkyo, Kenwood, Pioneer, etc) as if the AVR is the cause. I suspect that people who buy these AVRs are more likely to have surround sound setups (vs stereo or using TV speakers), and therefore are more likely to want to use Dolby Digital - at which point they encounter the issue with this encoding or re-encoding to mpeg4.
It was crystal clear to my that my AVR was not the cause because my Xbox360, Blu-Ray player and PC connected through HDMI do not suffer these issues on any material, and this issue does not happen on my OTA sources (which also go through my HR20 DirecTV box!) - unless I am watching the mpeg4 encoded DirecTV re-broadcast.