OK, thanks.
If the view order is correctly stored in the "stereoscopy" field of the MKV header, BD3D2MK3D should recognise it already. That means that the correct view should be selected automatically in the first tab, and the red warning should not be visible any more.
Similarly, the 3D-planes assignments should be automatic if they have been implemented with "3d-plane" tags (as suggested by tebasuna51), but that needs to be confirmed because they may have defined another tag or used a totally different method. I will have a look this evening...
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