I set up a 3d comp scene (not even using the new Raytracer mode) in CS6, right click on the camera, choose Create 3D Stereo Rig, and the resulting left eye and right eye comps work, but the Stereo Comp is just empty. I went back to CS5.5 and it works perfectly.
I'm surprised, as this should work just fine. Can you give me any more details of what you were rendering? Can you check each of the 4 comps and make sure they are all set to the same renderer selected. If this doesn't work, can I send you email? I'd like to get the project file from you to see what is going on.