Buddypress was no longer network activated. (The Manage Signups page was still there.) After the WordPress 4.0.1 upgrade I experienced problems on my multisite. Deactivating Buddypress helped (although the problem may have originated elsewhere).
Network activating Buddypress fixes the Manage Signups page. Now I just need to work out the fastest way to deactivate it on 100 blogs!
Thanks Shane – Buddypress Tools was under Tools as you said, on the dashboard of my main blog. I checked all the boxes and ran it but unfortunately it doesn’t fix the permissions problem 🙁
Sorry, that didn’t make sense 🙂 The problem wasn’t the divs. It was that the button function outputs straight to the screen, rather than into a variable. Problem solved!
Fixed it by putting this in my theme’s function.php: