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I honestly don't know why that could possibly happen. I can't reproduce this issue on either of the test servers I have access right now (local and live) or our live site. Sorry, I've ran out of ideas :(

Actually there is no log we can use; IP blocking is not logged. From your description I understand that the automatic blacklisting works, as the IPs are added to the automatic IP banning table (otherwise you wouldn't see them in the Auto IP Banning Administration page).

I can also see that the automatic IP banning is the first thing to run in plgSystemAdmintoolsPro::onAfterInitialise(), which executes as the very first thing after your site loads, before any of the other security code gets a chance to run. I am also seeing that the way the auto banned IP tables is being loaded is completely fool-proof. The only part that might get in the way is the block expiration check, which what I described in my previous message. Since you have already checked that and also checked that it is the same IP being blocked but still raising security exceptions, I am left without any plausible explanation.