It seems that your server accepts HTTP but not HTTPS connections, so trying to test the certificate with external tools will likely fail.
The instructions you have followed are for “certonly” mode, so while your certificate has been retrieved for you, it does not mean that it has been installed. You might either try the “experimental” Nginx plugin (see the advanced section of those instructions) or configure Nginx manually.
As for updating twice a day - it is not about actual updating the certificate at that rate, it is about setting up a process that will check whether it is time to update. If it is - then it will happen.