I have installed letsencrypt-win-simple on my Windows 2012 R2 IIS 8.5 server. I was able to created the certificate just fine and it worked on the website. The bad news is the certificate that was generated overrode the certificates in the central certificate store. I am not sure why? It is possible to create the certificates and not have them automatically install.
Thank you for your reply but I do not believe that bindings are the issue. The other websites on IIS were using the newly generated certificate from letsencrypt instead of their original one from the central certificate store. The other websites on IIS binding properties showed that they were correct certificate but when the website was brought up the certificate was letsencrypt. Also if you are correct does this mean every time we create a new website that needs a certificate we have to use the --keepexisting parameter?