I can’t for the life of see how Connections could affect Disqus. Connections doesn’t hook into post comments, at all, it doesn’t even read/write to post meta data. So that’s a definite head scratcher. Can you create a test page with Disqus active and no Connections shortcode? Then disable Disqus for that page to see if Disqus turns off as expected. If it does, then add the Connections shortcode. Is Disqus still disabled or is it enabled even though it shouldn’t be? Or is it disabled as it should be? If it is disabled, toggle the settings once more. What happens?