It looks like a couple extra
\<a href="\</div">\</a>tags have snuck their way into my menu after the upgrade. It makes a weird area only on the first menu link that is clickable but obviously goes to an erroneous location.
P.S. I also had to add float:none to #logo-wrap in order for the menu to look correctly. It’s in my child theme. Don’t know if that is related or not. When I upgraded I deleted the entire AegaeusWP theme from wp-content/themes and replaced it with AegaeusWP from the new 4.0 download.