I don't like the answer at all, but it IS the answer so I'll need to stick with FFMPEG for big merging jobs I do INDEED add some transition effects at the begginning and end of the video (fade from and to dark) and sometimes a crossfade between clips. If we could disable that intelligent detection and let the application do what we ask and assume our mistake if that was not the way to go, this would be awsome.
Thanks a whole lot for your answer, VERY appreciated!