I get this too. It works fine for a few days then suddenly one morning all I get is 404 Not Found for any page in the wp-admin folder so I cannot get at the login page or the dashboard to administer the site. It must think I’m some sort of intruder and locks me out. However, there is no message on the iThemes log except a report of the 404 for the requested page (eg the login page).
I have two WP subwebs, one of which is a private testing site and the other is ‘live’ and linked to from my main (non-WP) site. What’s interesting is that the test site is completely unaffected – it’s only the live site that has this problem. Both have iThemes 4.5.6 and it’s set up pretty-much identically on both sites.
The only way to bring it back to life is to rename the plugin, log in, rename it back and re-activate iThemes. I got that solution after posting this problem on the general WP Forum as at that time I didn’t know it was iThemes-related. If anyone on here has more-specialised knowledge about these things, I’d be happy to hear from them.
I’m not convinced deleting and reinstalling it would fix things, but would probably be persuadable if it was guaranteed to to work. Is it possible to retain all the Settings when doing that?
Running WP 4.1 (although this started under 4.0.1) under the Weaver II theme.