I have a Panasonic Viera P55ST30 3D TV, Onkyo AVX-380 5.1 channel 3D capable receiver, and the Directv Genie receiver. I have a top of the line 3D ready HDMI cable. On only a couple of occasions, I could get the 3D stations to work. 99% of the time it tells me "This program cannot be viewed because this TV is not 3D capable". Thoughts and ideas?
Assuming you are using the Onkyo to switch HDMI, there are two cables involved. Are both high speed? Temporarily connect the Genie to the TV directly and see if the level of 3D acceptance is improved. That will narrow down the problem area to work on. Did you see the sticky note on use of the DirecTV remote with Panasonic TVs here?