I read on the Dolphin forums (Nintendo Gamecube and Wii emulator) that Nvidia 3d vision requires the application to use exclusive full screen mode and will not work in a window.
iZ3D works in a window (I did not try DDD).
Disable 3D Vision and try iZ3D in anaglyph mode (free) to see if it works.
Also most professional applictions use OpenGL to render their viewports, this makes both 3D vision, DDD and iZ3d unable to work.
Some professional applciation have an integrated Stereoscopic 3D mode called OpenGL-Quadbuffer (OpenGL-QB) this is an industry standard but only works with professional hardware (Nvidia Quadro, ATi FireGL, and professional 3D displays)
Desktop : Intel Core i5-750, 4GB RAM, ATi HD5870, Windows 7 64bit
Laptop : Intel C2D-P8600, 4GB RAM, nvidia 9700M-GT, Windows Vista 64bit
Displaying Zalman Trimon 22" and 106" Passive polarised dual projector setup.
Watch my Stereo3D gaming video footage viewtopic.php?f=3&t=2020