JR and Sue Ellen seemed really miserable in the early seasons. Then again they had already been married for 7 years when the show started. How happy were Bobby and Pam after 7 years?
Right they got divorced around that time. So it's not like that couple was as much of a "golden couple" as the show wanted us to believe either. I think most of the characters and relationships on Dallas had some sort of dysfunctional dynamics to them.
Then as for Jock and Miss Ellie. I think Jock was definitely JR's father. But I think he was conceived before they got married. I think Jock only divorced Amanda and married Miss Ellie instead since he had to do right by her when she was expecting his child.