So, the first issue, as I see it from what you posted in the new Scott members not in Genealogy Reports and the Register Report.
Question: Who did you start with on that Report?
If you used the Register Report, that is a Descendant Report based on the Person you had hi-lighted and whose name is in the Report Title.
Please do NOT relate the Index (F2) / LH Panel, with a Tree. That is your File. Not a tree. As I hoped I stated, maybe not clearly, in my File, I have MANY Trees. So, that index is everyone in your File.
The Extended Family Chart, in the RH Panel, what Check Marks did you have just above the "Generate Chart" button?