Hi Rogurt, also see here for some explanation of a similar other situation to your new fillet case:
http://moi3d.com/forum/index.php?webtag=MOI&msg=3557.5

That shows some illustrations on how the fillets between things with differing slopes will not actually align at the same endpoint as the edges - one side of the fillet basically sticks out a ways further than the other side. That's part of what increased the complexity on your particular case - the filleter seems to be messing up trying to deal with the little in between portions that would have needed to be built there.

- Michael