Thank you Barbara.
I definitely do not have any unlinked individuals. I was very careful not to leave any when I performed my "cull" on unrelated (to me) people in my tree. My problem has been caused by the fact that when you delete two people, say parents of cousins spouse, then the family data, marriage fact, date, place etc., remains in the database. It then gets transferred into any gedcoms you create.
I have checked the unlinked sources, as you suggested, and have about 2800 of them. Unfortunately there seems no way to select them all and perform a mass delete. It's a slow process otherwise.