> If you navigate directly to the http url for an article, it does NOT redirect
That would be your problem. As far as Google is concerned you are operating two different sites. Redirect all your old http URLs to the HTTPS versions of the same content. But it might be too late if that old http content is considered “gone” from Google’s index.
If you navigate directly to the http url for an article, it does NOT redirect, but if you goto http://www.mysite.com, it redirects to https://www.mysite.com
I also see that when I Google my site's content, the links in google are https://, which means Google now knows that my website is running https.
What may I be missing here?