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How are you enabling active stereo? Are you using quad buffering or some other method? Also, what is the refresh rate of your display and what is the frame rate of the Vizard script (press F4 to display framerate)?
The only built-in support for frame sequential stereo in Vizard is through quad buffering. When quad buffering is enabled Vizard will render to both left/right eyes every frame. It is up to your graphics driver to decide which frame is actually displayed on screen. The behavior I have seen with quad buffered stereo is that alternating frames are displayed to each eye. However, this all assumes that your render time is less than the refresh rate of your display.
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