For all other vhosts that are for port 443, can you verify that each of them contains SSLEngine On? For the file you posted, this is probably done via Include /etc/letsencrypt/options-ssl-apache.conf, which should contain that line, but if you have any other vhosts on port 443 that do not include that directive, this could be causing what you're seeing here.
If that's not the issue, take a look at this post: