Thanks for your bug report, and welcome to the Doom9 forums.
First of all, have you read the solution found by CaBleman
here? As he has explained, the culprit was the hardware acceleration. If you use DGMVCSource, you can simply edit the _ENCODE_3D_MOVIE.avs file, and change the "hw = 0" parameter at the end of the DGMVCSource command with hw = 1. (You can immediately relaunch the encoding, without having to redo the whole demuxing process.)
Note also that soon after that post by CaBleman, I have released v0.52, and, the same day, v0.53, with a new option in the Settings -> MVC Decoder menu. It is now possible to specify "auto" (the default that doesn't work for you), "disabled" (the setting that you should try) and "enabled" (that will almost certainly produce the same bug).
Also, you posted your bug report exactly at the right moment. I had the intention to release a new version of BD3D2MK3D today. Although I'm not sure, it is possible that it fixes that bug, because DGMVCDecode.dll has been recompiled with the latest Intel INDE toolkit. The software decoder in libmfxsw32.dll has also been fixed by Intel. I know already that the new versions of that 2 DLLs fixes all decoding problems encountered so far with the software decoder (and notably the famous glitches in Pacific Rim at 1:06:14 and in Flying Swords of Dragon Gate at 1:23:35). I don't have the required Intel hardware to test the hardware acceleration, but Frank has tested it on several machines, and it works apparently well on all machines with the up-to-date Intel drivers. (It might still be necessary to force the software decoding if your CPU doesn't have the right driver, or if Indel has not updated the driver for your model).
I will release that new version very soon, but I still have to fix a little bug. Please come back in a couple of hours, and try the new version. In the meantime, please verify if you have the latest Intel drivers for your CPU. When you will have encoded a 3DBD with the new version, please report here if the updated decoders work for your CPU, with and without hardware acceleration. BTW, what CPU do you have?