Sorry for the remedial question, but I have to ask; do you have 7 speakers hooked up? I ask because I went through a similar scenario with a 646 user last year, only to find out he only had a 5.1 setup, which won't trigger Atmos/DTS:X.
Assuming your setup is correct though, make sure you've gone in to the Onkyo settings and it "sees" all 7 speakers (should be under Configuration and will show 7.1 or 5.1).
Lastly, make sure the source (either streaming or BluRay player) has the right setting to pass Atmos/DTS:X.