Accessing the origin server directly works fine both over HTTP and HTTPS (ignoring the obvious certificate name mismatch) so I’m not sure what this issue has to do with Let’s Encrypt.
Your best bet may be to reach out to Cloudflare support, and also check that you don’t have any Cloudflare page rules setup. (and your site seems to be in “I’m Under Attack!” mode as well …, at least based on the captcha I receive every time I visit it).
Seems like you may have pressed too many buttons in the Cloudflare UI.
I checked it yesterday but I couldn’t write a post. Yesterday, and seems today too (the only difference is that right now, as @_az said, cloudflare is presenting a captcha) your ORIGIN server has redirect directives configured in your web server or some rewrite rules which are redirecting your site as @stevenzhu commented a few posts above. If you are using Flexible SSL you MUST remove these redirections from your ORIGIN server or you get an infinite loop (as you are observing right now). You could also switch to Full SSL if your origin server has a certificate or switch to Full SSL (strict) is your origin server has a valid certificate.
Whatever, the best approach is to review your redirection/rewrite rules on your ORIGIN server and drop them.
Did you restart your nginx?. Are you using Flexible SSL, Full SSL or Full SSL (strict)?. Do you have any page rule configured in Cloudflare for your domain?.
As @_az said, if you are using Flexible SSL on Cloudflare use @_az, suggestion, if you were using Full SSL you shouldn’t need to create a server block listening on port 80.