I have had that problem (all black frames) only once, when I've tried to update libmfxsw32.dll from the INDE 2015 (a recent development toolkit of Intel). It appears to have a bug causing that problem with DGMVCSource. The bug happens only with some 3DBDs. (In my case, I've noticed it with Creature from the Black Lagoon.) I've tried less recent versions and the new 2016 version too, and they have the same bug. So, finally, I kept the version that is still distributed with BD3D2MK3D (v6.14.11.28 from Nov 2014), that works fine. Curiously, FRIMSource doesn't have that problem when it uses one of the bad libmfxsw32.dll. I don't know why.
If you have an Intel CPU that supports the hardware optimisation, chances are that you have installed the driver, and therefore the libmfx
hw32.dll installed with the driver is used instead of libmfxsw32.dll. And if it's a recent version, it has probably the same bug.
So, I suggest to try to encode in software mode (Settings -> MVC Decoder -> Hardware acceleration -> Disabled), or to try the other MVC decoder (Settings -> MVC Decoder -> Use FRIMSource). Note that you don't need to wait the end of the encoding to know if the decoding works correctly. If the process is much faster than usual (after, say, 5% of the encoding), that means probably that x264 is encoding black frames. You can also try to encode
this short sample (from Creature from the Black Lagoon), to verify if you are experiencing the same bug.
Please try the two solutions above, and report if they worked. I'm also interested in the title of the BD3D that causes the problem, and if you have experienced that problem with other 3DBDs as well. Thanks in advance.
For more information and the history of this bug, see
this report of the bug to Donald Graft, the author of DGMVCSource, and the last paragraph of
this post, where I explain why I haven't updated libmfxsw32.dll.