The problem wouldn't be the glasses; as you mentioned, they're passive. It's the light coming from one of the projectors that's switching polarity. If both projectors are actually displaying an image when this occurs, then the fault lies in the demuxing solution you're using.
A follow-on question to anyone who knows: where can you actually purchase a Geobox? The VNS website is useless (and clearly in Taiwan), and I can't find an outlet anywhere that sells them.