Noindex, nofollow stuck on homepage

The setting is stored in the options table under the key blog_public, the value is either 0 or 1. You can see the value of all options by manually visiting the page /wp-admin/options.php.

A quick way to get rid of it would be to remove the noindex action hooked to wp_head, which is what outputs that tag if blog_public is 0:

remove_action( 'wp_head', 'noindex', 1 );

This behavior is a bit strange though, I suspect perhaps something else may be involved here beyond simply the value of this option.