When you are trying to put together a family, it often helps to understand naming patterns. Different cultures have different customs when it comes to the naming of children.
The Dutch, as a rule, named the first two boys after the grandfathers and first two girls after the grandmothers. Parents, siblings would follow.
Unfortunately, the Welsh followed a similar pattern. The children were named for the paternal grandparents, maternal grandparents, then the eldest brother [husband] and sister [mother].
Christopher St. John was the father to ten children:
Mathias: paternal grandfather, Mathias [Du]
Joane: wife [Du/Eng]
Katherine: paternal grandmother, Katherine was Mathias' wife [Du]
Thomas: Christopher's uncle Thomas [Du]; father [We]
Elizabeth: ??; grandmother [We]
The parentage of Christopher's wife Joane and his mother Katherine are yet unknown. Sarah and Elizabeth could well be grandmothers. Roger, James and Humfrey could be candidates for Joane's father, grandfather and brother or an uncle. They are more English than Dutch. Nicholas is probably named for Christopher's family.
So there it is! Confusion!