I often get questions for various issues with 3D Vision not functioning properly and in most of the cases the issue is caused by having multiple displays connected to a PC. So if your new 3D Vision setup is misbehaving and not functioning the way you expect it to and the way it should normally work, then the first thing you need to think of is if you have a second display connected to the PC. The easiest way to diagnose if the issue is caused by the second display (this goes not only for monitors, but for TV sets or projectors as well) is to simply physically disconnect the extra display from the video card and see if 3D Vision will function properly. Just a reminder, the 3D Vision-Ready monitor needs to be set as primary in order for it to function properly for playing games in stereoscopic 3D mode or viewing 3D movies, so be sure that this requirement is fulfilled as well.
Now, if you find out that your additional display is causing the problems with 3D Vision you don’t have to disconnect and reconnect it physically form the video card all the time. You can just disable it through the Nvidia Control Panel when you need to use the stereoscopic 3D mode and after that you can simply re-enable it. Just go through the Setup Multiple Displays menu in the control panel and unckeck the display(s) that don’t support 3D and everything should work just fine. Now, in theory if you’ve set the 3D monitor as primary you should not have trouble even if you have a second display connected to the PC, however in practice this doesn’t always happen.