I also changed my nickname and asked wordpress to use it for public display. I've no idea whether this has anything to do with anything, but I'm offering some info on my site's configuration so someone might help:
I had changed my wp_content folder's name prior to the update
I had hid my htaccess file prior to the update
I had changed my database prefix prior to the update
I clicked "save settings" several times after reviewing them and thinking them exactly the same as before"
That seems to be the most critical aspects of my Better WP Security settings.
Before upgrading I had to upgrade my theme and a couple of plugins. The last plugin I updated was WordPress Seo by Yoast, the only plugin I updated after upgrading to Ithemes S.
I also added a couple of lines to htaccess to increase execution line, but erasing them doesn't fix the problem, so I think it's unlikely they are the cause of it.