Auto SSL from user account does not work...but does for user from root dashboard

Issue 1.

If i attempt to install an AutoSSL from user account, it says its updated successfully, however, when i check on the front end (ie a wordpress website for example), there is no SSL.

If i then go to the root administrator CWP and create an SSL from there for all domains, then voila, wordpress now detects SSL for the domain and works as expected.

I am confused by this?

Issue 2.

Also, even though the user domain now has a valid SSL, in CWP.user dashboard>Domains>AutoSSL, there are no valild SSL certificates listed (when i select the users domain, SSL area below is completely blank.

Can someone advise as to what is causing the above 2 issues?

I think that you are using Apache only server , Auto SSL is working perfectly with NGINX server on CentOS Webpanel .

For Apache only web server , Follow the Guide :
 http://forum.centos-webpanel.com/ssl/install-let'sencrypt-for-admin-panel-user-panel-again-100-working/

My default webserver is nginx + php-fpm