However, since other players like VLC didn't show them, I was not convinced that this was really a bug.
Then again, lately I checked one of the newer conversions on an old tube TV with a Popcorn Hour media player and observed strong interlacing.
I'm still not convinced that this is really an issue of BD Converter, but maybe it's worth to have a look.
As a side note,"DGIndex" aka "DGMPGDec" shows interlacing as well:

To me it looks as if the field order was swapped, but some players seem to ignore it or automatically detect the wrong order and show the correct frames.