First of all I want to say what an amazing plugin this is.
I seem to have found a bug in the htaccess code that is built for hiding the backend.
If you have a MS setup and are using domain mapping (sites on domains instead of subdomains of main site) it's going to kick out everyone that's logging in to any of the subsites.
Even though they're going trough the secret key / secret login page.
Also unrelated: you can't rename admin ID #1 if MS is turned on. The option is missing.