Just wanted to update this: I've got 3D to work on the latest version of Dolphin using the 'Passive' option instead of using the 3D vision option. Games won't launch at all if you launch Dolphin with stereoscopic 3D enabled in Windows/Nvidia CP settings regardless of the 3D rendering option setting in Dolphin FYI. Thanks guys. Would still rather use Nvidia 3D vision but hey it works.
Edit: Games not launching with 3D in Windows/Nvidia CP turned on is only when using DX11.
Edit: Games not launching with 3D in Windows/Nvidia CP turned on is only when using DX11.