Is there a way to change the background color of the verse reference pop up window ??

The popup will have the background color of the relevant active view.
So if the link is in the Bible view and it is an xref or footnote will have the popup color of the color you have set in that view. A Strong's number in the Bible view will use the background color of the active Bookview. If the link is in a Bookview and it is a Bible verse reference it will use the background color of the active Bible view.

So you have to set a background color for each view you have. In the Bookview it can be changed via a menu option under the green library icon top left of a Bookview. For the Bible view there is the option by clicking the gear icon on a Bible view.

Seems like I have been through all of these.... I was hoping for an option to make the pop-up window totally different from Bible view and Book view so that when it pops up it would really stand out from everything else...... Hope I am not misunderstanding your instructions ?? Thanks....

I think you got the idea.
If you want to have the views with a color but the popup white, you could do as I do. I put a background picture that is a slight beige color, and keep the background color white in all views.

..... YES,,,,YES,,, why didn't I think of that !!!! Thanks so very much !!!!!