Good luck. Appears to not be a Channels DVR issue.
I've just been on an Odyssey with Shield 9.1 and trying to get various films with multichannel sound working on my 5.1 setup going to a Pioneer AV receiver. There's quite a lot of things that need to be correct for a 5.1 or 7.1 channel film to pass through correctly.
The first possible breakdown is the auto-negotiation of permitted audio formats between Shield and the Receiver. Settings->Device Preferences->About->Status->HDMI->Audio Mode will tell you which audio formats Shield has auto detected. Any audio type not listed will be sent as 2 ch stereo. For the Pioneer Receiver I had, it did seem to negotiate the list correctly.
It is possible to override the detected audio settings and set which formats are passed through and which are downmixed to stereo here: Settings->Device Preferences->Display & Sound->Advanced Sound Settings->Available Formats
At this point you should be able to go to the YouTube app and find some Dolby 5.1 test videos and confirm it works. However, for me, anything above 5.1 plain Dolby Digital (AC3) was being rendered to stereo. Even though my receiver supports 7.1 and more advanced formats (but not Atmos).
The key to making it work for me was turning off Dolby Audio Processing in Shield, that's enabled by default. It can be found here: Settings->Device Preferences->Display & Sound->Advanced Sound Settings->Dolby Audio Processing.
With it turned off, it appeared to send through some formats as PCM 5.1, while other sources were various Dolby formats. Completely incompatible formats with my receiver like Atmos and DTS-X were still rendered to stereo. Supposedly Dolby Audio Processing is supposed to increase backwards compatibility by converting more recent formats like 7.1 Dolby Digital Plus to lowest common denominator 5.1 AC3. However, a number of people have found it to cause trouble and far from helping compatibility, it breaks things and found relief from disabling it.
So finally I have my audio not being converted to 2 ch stereo for most media. This might work for you too.