I’m running a VM with windows server 2012 R2 and IIS 8.5 and I have multiple websites configured (on the same IP) and multiple subdomain-websites. I tried running Certify and Let’s Encrypt Win Simple, but the same problem occurs for both.
When I select 1 website to create a cert. and update the IIS bindings it works fine, but when I continue to the 2nd website, it works again, but then it also removes the binding from the first website again, and updates it to the same binding as the 2nd website. It seems that I cannot get multiple certificates with each unique bindings in IIS, resulting in that I can only get LE to work with 1 website at any time.