I've just upgraded BE.NET to the final 2.0 version (was running RC for the past couple of weeks as well). In both versions, with Disqus comments enabled, I was getting the following notification when accessing post comments:
"You are seeing this message because developer mode is on. One or more of the following embed variables are missing: disqus_identifier, disqus_shortname. They are recommended for stability reasons, read about them in the Disqus Developer Docs"
Scanning for new reactions didn't work either.
However, modifying a post file template (e.g. post.aspx) to the following (to include required variables):
var disqus_url = '<%= Post.AbsoluteLink %>';
var disqus_identifier = '<%= Post.Id %>';
var disqus_shortname = '<%=BlogEngine.Core.BlogSettings.Instance.DisqusWebsiteName %>';
var disqus_developer = '<%= BlogSettings.Instance.DisqusDevMode ? 1 : 0 %>';
dsq.src = 'http://<%=BlogSettings.Instance.DisqusWebsiteName %>.disqus.com/embed.js';
(document.getElementsByTagName('head') || document.getElementsByTagName('body')).appendChild(dsq);
... seemed to have resolved the issue - the reactions are shown, but there still are some issues with showing the correct number of reactions in the other places I didn't go into.
I believe this issue is a result of a recent Disqus API changes... Anybody have a more complete solution?