Make sure all the power supplies are plugged in and working.
In another thread where someone reported a similar problem, it was determined that although the documentation for their baluns and switches claimed that their external power supplies were optional, they actually were required. When power was connected, the glitches went away.
Have you tried inserting HDMI extender "amps" in the cable runs connected to the 3D TVs?
Of course, the extenders would have to be rated for the bandwidth needed by 3D. HDMI video glitches usually are caused by the display receiving a degraded signal. 3D requires quite a bit more bandwidth than 2D does, so would tend to be more sensitive to marginal signals.
I've experienced dropouts in 2D 1080p60 video which didn't affect the audio, so by itself I don't think that's a very helpful symptom.