It seems that Better WP Security 3.3 and WordPress 3.4.1 may not be able to play nicely together.
After functioning well for a short while, today Better WP Security pretty much took down my whole website, and sent me over 600 emails to tell me about it.
Each email said "A file (or files) on your site at http://www.mydomain.com have been changed. Please review the report below to verify changes are not the result of a compromise." There was no report to look at, but there never has been since I installed the plugin.
When I went to my website, my front page was a 404. When I logged into WordPress as admin, it told me I had 0 posts, 0 pages, 0 comments... phpMyAdmin told me otherwise - nothing had changed.
When I looked at my website file manager, I saw that no files had changed there either - not even my .htaccess. I renamed the wp-better-security folder in my plugins to disable it, and removed all reference to Better WP Security from the .htaccess file.
I was relieved to see that my site started working correctly again, and - thankfully - the automated emails stopped.
I love what Better WP Security had been doing so far, and I had some peace of mind that it was running (aside from the blank emails mentioned above; I'd been advised of bad login attempts and everything) - but this was pretty stressful and I'm hesitant to re-install Better WP Security again until I know what may have caused this issue.
Just my $0.02 in case something similar happens to your site.