Thanks for the reply.
Yes, HDMI is the only connection being used. I rip the audio as passthrough audio, so it is taking the original ac3 audio stream from the DVD. I rip to mkv, and use cccp to playback (so ffdshow audio decoder gets used). I have the volume normalize effect turned on in ffdshow but have made sure that nothing else is ticked (so that the number of channels from the source isnt being messed with).
On the reciever I see FL and FR lit up on the left hand side of the display, and all the 5 channels lit up on the right. So it appears to me that it is taking a stereo input and decoding it to surround. That's what has me worrried, because the source file is definitely surround. When I look at the mixer in ffdshow audio decoder I can see in it's channel matrix that each of the 5 channels is having sound pumped through it (though they are all greyed out because I dont have the mixer turned on).