Thanks for your kind words, Kuvenant.
Are you sure you are using the latest version (v1.19) ? There is a known bug in old versions of the FRIMSource MVC decoder, that produced a 2D stream when the left and right views are inverted in the original 3DBD. That bug has been fixed, and the last versions of BD3D2MK3D distributes the correct version of FRIMSource.
Note also that DGMVCDecode has not that bug, so if you have still that decoder, you can use it instead of FRIM. See Settings -> MVC Decoder. DGMVCDecode has been removed from the current distribution, but if you do not remove it when you install the new BD3D2MK3D, it will still be available. However, it has been discontinued by its author, and I don't support it anymore.
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Well, I was using v1.18. Deleted it completely, installed v1.19, and everything works great. I'm guessing I must have replaced only the application and not the toolset when I updated previously. So it was a fairly obvious fix. Thanks for your help.
Now the only 3D videos I have left to fix are 'The Drawn Together Movie: The Movie' and 'B.O.B.s Big Break'. Turning anaglyph into stereoscopic will be a blast.
Thanks for the confirmation.
Bob's Big Break (the short animated clip) exists in true 3D. It is on the Monsters vs. Aliens 3DBD. I don't know The Drawn Together Movie: The Movie. And converting anaglyph to SBS or TAB is really difficult. I have tried with Shrek 3D : the adventure continues, but although the 3D is perceptible, it is a pain to watch that relatively short movie, because the luma changes randomly in the two views, and the color is not uniform. Good luck !