I would agree with "garcianc", because I've had similar problems with my Scientific Atlanta 8300 DVR and my Sony receiver. You said you had your Cambridge receiver set to "auto-detect" the type of signal it was getting, right? The drops-outs are most likely cause by the fact that commercials are almost ALL in 2-channel stereo, whereas most HD programming is broadcast in either Dolby 5.1 or DTS 5.1. When the broadcast changes from stereo to 5.1, the processor has to figure out what type of processing to use, and if your signal from your dish isn't dead-on perfect, it might cause the receiver's surround processor to sort of stutter while it's trying to make up its mind.
If you can set the digital sound output mode on your DVR (through it's setup menus), set it to just automatically default to send EVERYTHING as either Stereo or Dolby 5.1. Then, if you've picked "stereo" as the DVR's output type, set your receiver to some sort of "synthesize" 5.1 format, and let the receiver's processor create the missing channel info from the stereo signal. If you set the DVR to "Dolby 5.1", set your receiver to one of it's Dolby 5.1 settings. IF they are both the same, the audio dropouts should stop.
Some of the older receivers and Pre/pro units has slow processors, and they sometimes will take a while to determine the format of an incoming signal, and this "processor lag" sauses the receiver to automaticly dial back (or even shut off) output to your speakers until the processor gets a lock on the signal. The newer units seem to have utra-quick processors, and almost never display this phenomena...
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