Upon the most recent update the search box is no longer functioning. The input box is offset from its display window. I am not sure what caused this but when reverting the site before the most recent update to your plugin, it was working.
It looks like the menu script might be adding some line breaks to the empty lines of the source code. It happens because most menus may expect text content within the widget and not HTML. If you can change the container widget type from text to HTML, that will resolve the issue.
If not, then adding this custom CSS will do the trick too: