Post and Portfolio Category Noindex set?

Hi, I noticed that post and portfolio categories were automatically set to noindex. When I go to the edit category, there are check box for noindex and no follow. Those boxes are NOT checked. (The boxes look elongated; not like reg checkbox)

I am using Infinite SEO which lets me set those separately. Can I comment out this line in the header?

/*
 * outputs a rel=follow or nofollow tag to circumvent google duplicate content for archives
 * located in framework/php/function-set-avia-frontend.php
 *
 * if (function_exists('avia_set_follow')) { echo avia_set_follow(); }
 */

Thanks for your help.