This is a strange issue. I recently fired up a new VM web server running Ubuntu 16.04.2 LTS. This is my first time using EasyEngine, and so far, I absolutely love it, save for some random issues, most of which I tracked down to Cloudflare (which I have since removed).
I've set up 20 or so sites, with about half of them being Wordpress sites, and most of them being development sites, or archives of old sites for my portfolio. Everything performs great and behaves as expected, but with one random strange issue.
I have a couple of subdomains that LetsEncrypt will just not issue certificates to. Nothing is behind Cloudflare anymore, although all my sites were able to obtain LetsEncrypt certificates with Cloudflare active except for these 2 subdomains.
The configuration files for these sites are fine, or so it appears anyway, since they look the same as all my other sites that work fine. DNS for both the subdomain and www.subdomain are configured. But every time I try "sudo ee site update subdomain.mydomain.com --letsencrypt" I get the message:
Unable to setup, Let's Encrypt
Please make sure that your site is pointed to
same server on which you are running Let's Encrypt Client
to allow it to verify the site automatically.
At first I thought I might have hit a limit for how many certificates I can request in a period of time, but if I create another site/subdomain, it gets the certificate right away without a problem.