Try power-cycling the eMagin, then fire up Vizard with Quad Buffering. Perhaps the eMagin just needs a few tries to get synced with the active stereo signal.
By the by, viz.go should include the HMD argument for proper stereo disparity. I don't think this will fix the flickering in the eMagin though.
Code:
viz.go(viz.HMD | viz.QUAD_BUFFER)