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If this occurs cyclically without any input to Vizard (e.g., just staring at the window), then the issue seems unlikely to be Vizard related. Rather, I would guess you’re having a sync issue across your projectors. If one projector doesn’t maintain perfect gunlock with the others, then your shutterglasses (being held in sync with other projectors) will give the appearance of sometimes positive stereo, sometimes negative stereo, and sometimes neutral (no) stereo.
Do you have an independent application (not Vizard) that reproduces this phenomenon (or fails to produce it)?
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