Since OpacMoreSearches was moved from a system preference to a HTML customization it creates invalid HTML with a <div> directly inside an <ul> element. Furthermore, the WYSIWYG editor of the HTML customizations doesn't allow you to add <li> elements without a surrounding <ul> and automatically adds these "missing" elements on saving. So the original intent of having the navigation items being <li> items within the existing <ul> of the navigation isn't working anymore.
*** This bug has been marked as a duplicate of bug 39974 ***