I currently have Let’s Encrypt installed on my Ubuntu 16.04 server. I had to reinstall the ssl certificate and edit the conf file in sites-available as the domain changed. The domain is working both with http and https, however, this was generated in the report for www and non-www:
I can't see any outage/issue regarding ocsp in https://letsencrypt.status.io/ and I tested it a few minutes ago and I can check the ocsp response for one of my certs.
Can you connect to http://ocsp.int-x3.letsencrypt.org from that Ubuntu server?.