I have a similar problem.
One additional problem is that the Admin cannot access the site-wide report logs. In fact, Logs does not appear on the Site Administration/Reports menu.
A further symptom is that within a specific course the Admin can select Reports and view the Logs by choosing that course (or any other course) from the the drop down menu. However, when I choose the entire site, I get an "Access denied" error.
It seems obvious there is some role confusion, but I have not found a remedy.