tchamberlain, I am trying to do exactly the same. I want to protect some content on whsramsfan.com and I want to use the wp-users table for identity management. can you share the answer that you found? thanks.
I recently upgraded to 2.6.3 and now I am experiencing the same issue. When I approve a comment, it is removed from the list, but it will not show on the post. when I go back to the comments list, the the same two are back again as unapproved.