For others who want to try it...
I have a Quadro M4000, glasses and a monitor that does 3D @100 to @144 Hz. I found I needed to make a special setting in the NV Control Panel for CloudCompare. Click Manage 3D Settings, then select the Program Settings tab. Click Add and choose CloudCompare from the list of programs.
I think the very minimum you need to do is force Stereo - Enable to ON so the emitter light goes bright green when you start CC.
It will be nice when it works in regular mode too, instead of just full screen.