Currently we need to manually diable it, publish the web site and then manually re-enable it again.

I am also having an issue with the site content being lost after returning from the blog. If I log out then back in, the content is back. Is this part of the same issue? What it means to me is I can't use the authentication at all until it is corrected.

No. This is HTTP authenication, it is not login from login box. Regarding to your issue, please submit support ticket and describe step by step to duplicate the error. Our developers will take a look.

This does not work well either. When I do this, then visit the blog, the rest of the site content goes away! This is not a good work around!