Cortona3D Viewer uses graphics cards capabilities and we were able to show stereoscopic content using NVidia Stereo driver and DirectX rendering settings. Below are the steps, that we used to see stereo 3D.
1. Go to NVidia website and download 3D Vision driver for your OS
2. Install NVidia 3D driver
3. Open NVidia 3D stereo panel
4. Choose 3D stereo enable
5. Check resolution
6. Start Cortona3D Viewer
7. Open Cortona3D Preferences: Check DirectX, Enable Pixel Buffer Access
8. Choose full screen mode
Please try changing the rendering mode in step 7 to OpenGL.