I have an SA 3100HD box and haven't had that problem here with Time Warner Cable but have noticed it at my sister's place in FL (Comcast). I assume your box is similar to mine and has a setting for 'digital audio out' which is set to Dolby Digital - not 'other' (in my case, 'other' means PCM).
I think the problem lies with the receiver but it could be a setting in the receiver that causes it. Does that receiver allow you to set the 'default' decoder for various formats? For example, you can tell it that for 2 channel PCM, always use PLII and for Dolby Digital always use the DD decoder.
I think what happens is that you are receiving say a DD 2.0 broadcast and the receiver correctly switches to the PLII decoder but then the signal changes to something else like 2 channel PCM and it switches to whatever decoder is set as your default for PCM. But then when the signal changes back to the original DD, the receiver doesn't change the decoder like it should. With Comcast in FL, that is the behavior I have observed - watching a DD 2.0 movie and then a commercial comes on that is PCM, the receiver switches to PCM but for some reason doesn't switch back to using the PLII decoder when the DD 2.0 movie resumes.
You might want to check the menu to see if you can set default decoders for each signal type and set anything that is not DD to use PLII as the decoder.
