When a single IP address can support multiple virtual hosts, probing port 443 for an SSL version of a domain is naive and may trigger an intrusion detection system (IDS). Sure, you may get a response (and even the same content), but that's no guarantee that the domain you used is configured for SSL on the server. An IDS may flag the request as a potentially malicious probe and temporary block the IP address from accessing some resources. This can be extremely useful for blocking exploit attempts by drive-by bots that request by IP address alone. Of course, it would be strange to continue to allow access to the SSL resource as in your example, but maybe there's a reason for it (server admin has different goals than site admin, for example). Just one possible explanation. You might regain HTTP access if you stop hitting HTTPS for a while.

Edit: The CN in the cert is news.ycombinator.com, so it's unlikely my explanation is the cause (but still could be).