After I upgraded the disqus plugin to 2.41 I got inundated with comment spam. I was wondering what was going on until I realized that somehow, the spam comments that disqus had been blocking were now making their way - as spam and not as actual comments - into my WordPress comments. I checked the disqus comment spam and they were not there.
I have since rolled back to version 2.31 and this spamming has stopped. Clearly, the 2.41 versions and above were interacting with my comment system in a way that required the WordPress system to filter spam instead of disqus. Is there any way to change this?