So, this is clearly a late reply, but I just ran into this issue with the Nightmare Before Christmas 3D Bluray, though other 3D movies play fine. For starters, I have a 2011 58" 8000 series Samsung Plasma with an original [Fat version] PS3 and of course using a high-speed HDMI cable.
The issue was, when I booted my PS3 it recognized that I had a 3D TV, but when I loaded the DVD, all I could get was a blank screen after 2 seconds of loading dialogue. Of course I checked everything like Display Settings, Swapped the HDMI cable, and power-cycled the PS3 and TV numerous times without resolution.
Then it hit me, Sony sucks so they probably botched the software! So I went to the Display Settings on the PS3 and changed my TV size to a 56" and wouldn't you know it, the damn thing works.
So if you are still having this issue with some 3D movies, you may want to try adjusting your TV size settings in the PS3.