Here is what happened with me:
2 different devices (Nexus 7, Galaxy Nexus)
Using Netflix, I used the movie "Super 8" as a test, since it has 5.1 audio normally.
When streaming on the Chromecast, initiated from the Nexus 7: only stereo, and that is my only selection option.
When streaming on the Chromecast, initiated from my VZW Galaxy Nexus: I can select from stereo, or 5.1 DD+. The later gives me full surround sound.
Both devices have up-to-date Netflix apps. Both devices are stock, and not rooted.
EDIT: I reset everything, and it seems to be working now normally when initiated from either device.