It's not in the GUI, because BD3D2MK3D trust the BD, but you can change the order of the views manually.
Just generate the project normally, but before launching the encoding, edit the file __ENCODE_3D_MOVIE.avs in the project folder with a text editor or notepad, and change the following lines:
Code:
left = SelectEven(interleaved)
right = SelectOdd(interleaved)
to this:
Code:
right = SelectEven(interleaved)
left = SelectOdd(interleaved)
Or the opposite, depending of the order stored in the MPLS file. The idea is to swap the left and right streams just by swapping their names.
That should work.