Well I assume your receiver in your sound system has HDMI v1.3 because of its relative newness on the market, so your receiver shouldn't be the issue. It sounds like the problem lies within the cable box.
The Motorola HD-DVRs are notorious for having problems when connected to a receiver. This is because your HD-DVR has anti-piracy code in it that sometimes detects your receiver as an unauthorized recording device and then will not allow anything to be sent to it for fear of piracy. But in your case, you are getting video and audio to your receiver without an error message.
You might have a faulty HDMI cable. If you can borrow one or have another one on hand try using a different one to see if anything improves.
If that doesn't do anything you might need to goto monoprice.com and buy one of their HDMI v1.3 switchers so you can run HDMI from your cable box and from your sound system receiver to the switcher, and then one HDMI cable to your HDTV. And then run a digital optical audio cable from your cable box to your receiver for audio.
The switchers aren't very expensive and should fix your problem (if it isn't a faulty HDMI cable). If the problem persists even with a switcher I'd say your HD-DVR is malfunctioning. And since you said your DVR sometimes is unaccessible, I'm leaning towards a bad HD-DVR as part of the problem.
To troubleshoot I'd try these steps (in order):
1) Try a different HDMI cable from your cable box to your receiver
2) Trade your HD-DVR into Comcast for a new one and see if the problem persists.
3) Buy the HDMI switcher from monoprice.com (make sure it is v1.3)
I am not an audio or videophile. I have no clue about anything. All I know is I like to watch a nice picture with nice sound. I have a 46 inch Sony Bravia LCD tv. I just purchased a Sony SF2000 surround sound system that can take 3 HDMI cables. I bought it because my Bravia tv is old and only has one HDMI input. I plugged my PS3, Sony upconvert DVD player, and Comcast Motorola HD DVR box into the receiver (via HDMI cables)... and then the receiver (via HDMI) goes to the TV. Now the video quality of regular tv is much worse going through the receiver than if I connect the comcast cable box directly to the tv. On top of that, when I am on an HD channel, and then switch to a non-HD channel, the audio comes through my receiver, but the TV goes black (no video). I have to then turn off my Comcast HD DVR box, turn off the tv, and turn off the receiver, and then turn everything back on again. Does anyone else have this problem? Another problem I have now is that my shows that were saved on DVR are no longer accessible. What is going on? So a couple questions.
1. Is it normal for video quality to decrease when routed from cable box to receiver to tv as opposed to going directly from cable box to tv? The picture is 10 times granier than before. Are my HDMI cables too crappy? Do I need to buy higher end HDMI cables? I have 6 foot HDMI cables. Should I buy 3 foot HDMI cables?
2. Why does my video go black when I switch channels from an HD channel to a non-HD channel? Is my new receiver not picking up some kind of a signal?
3. What is wrong with my DVR? It no longer plays my recorded shows. Is the problem with my motorola box? I've had the motorola box for maybe 20 months. Time to get a new one?
4. Did I just waste my money on a Sony SF2000 surround sound system where I am now sacrificing video quality for audio quality?
Please help. Any suggestions or opinions are greatly welcome.