Well I just installed the big map mod and the family tree problem seems to have sorted itself out. I married my vision of beauty passionate woman princess to a HRE general, and he has a son, daughter and 2 adopted sons. The whole family is on the tree, although the biological children have English surnames - rather than 'von Saxony', one is called 'of Selwyck' and one is called 'Pole'. No matter, this guy is delighted with his wife.