Hi, welcome to the Doom9 forums.
I have never encountered that kind of problem, so I don't know how to help.
If your output movie is blank, I can only suspect something wrong with your Avisynth installation.
I suggest to install
AvsPMod. It's an avisynth script editor. Open the _ENCODE_3D_MOVIE.avs file in AvsPMod, and click the up arrow in the bottom left corner of the main window to launch the rendering. You should see the first frame of the movie (usually black). Use the right cursor key on your keyboard to play the next frames. After some frames, you should see the video beginning to play.
In AvsPMod, you can also click the Play (right arrow) button to launch the preview of all frames, but that button doesn't work always well.
Do NOT use the seek bar or the input field to jump directly to a specific frame, as the MVC decoder doesn't support seeking, and will hang. If that happens, close AvsPMod and relaunch it.
(Note also that the script may not work in AvsPMod if you have selected the option to hardcode subtitles on the video, because AvsPMod may not find the subtitle decoder plugin. So, test without hardcoded subtitles.)
You can also test avisynth by loading the "Test_Avisynth_Installation.avs" script in the "toolset" folder of BD3D2MK3D.
If the script doesn't work, try to use the other MVC decoder. (Change it with Settings -> MVC Decoder.)
If you can see the video in AvsPMod, that means that avisynth is working correctly, and I don't understand why you obtain blank frames. Otherwise, try to re-install avisynth. (And be sure to install the 32-bit version.) You may also have to remove the additional plugins from the Avisynth plugins folder, if you have installed special plugins manually.