HTML in a widget

That’s weird, that shouldn’t be the case:

/** Only display if title is within the main loop */
      if(secondary_title_get_setting("only_show_in_main_post") === "on") {
         global $wp_query;
         if(!$wp_query->in_the_loop) {
            return $standard_title;
         }
      }

Put this in your theme somewhere and check if it returns either “on” or “off” so we can see if the option gets saved properly. If yes, it could be a design-issue with your theme.

<?php echo secondary_title_get_setting("only_show_in_main_post");

If you send me the theme via e-mail ([email protected]), I can try to find a solution.