I'm not a 3D vision user so I'll just ask if you usually have freezes when playing games without 3D as well. It could be the same thing, a temporary lockup?
Anyway I doubt there are many 3D vision users here... maybe you'd be better off asking this on a Nvidia forum, or sending a mail to Nvidia directly.
My Mario Kart Wii friend code: 2707-1866-0957