I’m experiencing similar issue with domain validation.
Domain has two A records with different IP addresses (DNS round robin) but website is accessible on both of them. Server is IIS 10 and Lets Encrypt is being renewed by control panel (MSP Control) or by external software (https://certifytheweb.com/). Both of certificate requests (control panel and software) end the same. They can’t validate domain. IIS server logs show that there was external attempt of validation with 200 status from IIS server:
2017-10-16 09:58:09 188.8.131.52 GET /.well-known/acme-challenge/Kg-YkYXMtRXzyejWlVSwE8OyWfCndN_000LLLyrf-KU - 80 - 184.108.40.206 HTTP/1.1 Mozilla/5.0+(compatible;+Let's+Encrypt+validation+server;++https://www.letsencrypt.org) - - web.arena.tituto.com 200 0 0 564 272 179 -
this one is last example when I was trying to create certificate request from Certify app. Website has empty page and no redirects (web.config or .htaccess). Latest file in acme-challenge dir is still accessible:
Any ideas what is causing this issue?