BPS Alert: what to do?

I have updated the BPS plugin and since that I receive the “BPS Alert! Your site does not appear to be protected by BulletProof Security” message, recommending fix it through the Security Status page. I’ve read the Read Me’s in that section and it’s getting me even more confused. All my recommended permissions are updated, except root folder. Could somebody tell me, in simple words, what I must exactly do to put things in order?