Hi Mark,
May I ask how is that search bar placed to the menu?
I looked in the theme editor in functions.php, and I found a relevant code, however that is not it. If I disable the code the search bar is still present on the page.
I created a test search bar, and replaced that shortcode with it, and it is working fine. I assume the original search bar is placed there either directly injectin the HTML output of the search or via javascript. In the most recent versions, the HTML output has changed a bit, there is a container element added, without that the plugin can not initialize. In case you are directly outputting the HTML code of the search, then try to capture the new output first. However I do not recommend that method when avoidable, as using the shortcode will always get you the latest output, and it is the only supported use of the plugin search bar.