I think that you'll have to talk to the creators of the SEF extension.
Here is how ccomment works. When you visit the article, you'll notice that the comments are not part of the source code of the page. We load them through ajax. Because of that search engines cannot know that there are comments on the page. Fortunately there is a specification:
developers.google.com/webmasters/ajax-crawling/
which ccomment follows. The specs says that the search engine will add ?_escaped_fragment_=key=value to the url and then we need to show the content visible to the search engine. For some reason your SEF extension is adding this ?_escaped_fragment part and it's triggering the search engine view of the comment system.
Regards,
Daniel