The plugin uses a cascade approach so any settings in the global SEO tab will change the defaults for all pages SEO settings.
Check the global SEO tab and make sure it’s set to yes for indexing. If you still have the problem, check the config.php file to ensure there is nothing in there that is preventing indexing.
Lastly, the plugin will always disable indexing when the debug mode is set to true in the config.php file. If the website is live, you should always disable debug mode.