You might try updating and making sure you have (and run) the latest updates of the driver from Nvidia.
v.6.05 was the latest I found for that model, but you'll want to check with them for these compatibility issues.
I have a Samsung 60Hz 3D-ready DLP HDTV (Model HL61A750A1F). I also have a home theater PC (Intel i7-920 CPU w/ 6GB RAM, an nVidia GeForce GTS250 graphics card and Windows 7 64-bit operating system).
Because Samsung no longer sells 3D glasses for these 60Hz HDTVs, I have (1) an nVidia 3D Vision System emitter and glasses (the emitter comes with a cable for the 3D sync output on the back of the Samsung TV) and (2) a copy of just-released PowerDVD10 Ultra software which has the ability to convert regular DVD movies into psuedo-3D. I also have a 3D version of Avatar the Game that came with the nVidia 3D glasses.
Although the 3D Avatar game works perfectly with the emitter & glasses in 3D, movies do not. When I play a standard DVD and enable the 3D format in PowerDVD 10, the 3D video signal clearly appears on the HDTV screen as a double image; however, the emitter will no longer come ON to send the sync signal to the glasses.