I've been having this same problem, even after buying two different "high-end" high-speed HDMI 1.4 cables. Panasonic's support blames the HDMI cables too, btw. Frankly- I think that's BS. If it's that touchy- then there is something wrong with their HDMI jacks (on the TV or the player), and not the cables.
What seems to fix it most of the time is to make sure the TV is powered on and set to the correct HDMI channel FIRST, and then power on the Blu-Ray. The Blu-ray player doesn't seem to be able to auto-detect the 3D display after power-on.
This sucks, because it can't be set up that way automatically on my Harmony remote- so I have to toggle the power on the Blu-ray every time I choose to watch it. (It power on all devices first, and then sets the TV input.)
I think this weekend I am going to see if my 3D Sony BD player has the same issue. At least I can then narrow it down to the player or the HDTV.