I found I had some directory and python file permission issues so have updated the /www/server/panel directory to 755 and the files to 644. Seams to have fixed another issue, But no change on this SSL issue, saw this in the panel error log.
Starting new HTTPS connection (1): acme-v02.api.letsencrypt.org
Unable to intialise client. error=HTTPSConnectionPool(host='acme-v02.api.letsencrypt.org', port=443): Read timed ou
t. (read timeout=20)
38.98.196.227 - - [2019-11-06 09:01:27] "POST /site?action=CreateLet HTTP/1.1" 200 500 0.351013