Yoast SEO 1.2.5 – Duplicate title noindex/nofollow not working?

Hi I am running version 1.2.5 of the plugin on wp 3.4.1

I am experiencing duplicate site titles being indexed. I have checked the box “Noindex subpages of archives” but for some reason the setting is not taking effect. You can check my inside blog page @ http://www.shelbyvilleillinois.net/blog/page/2/ and you will see noindex nofollow does not appear in code. I am also running w3tc and have tried after all cache cleared still same problem. Any ideas what might be the issue?