Not sure if this will help you guys, but it fixed mine.
In your DISQUS settings from WP-ADMIN, click “ADVANCED OPTIONS” up top just under the logo next go “MANAGE”
Check the “Comment Count” [ Check this if you have a problem with comment counts not showing on permalinks (more info).] if unchecked.
If it is already checked this probably won’t work – hope this helps a few of you out there with this frustrating issue!
Gabe
NewHustle.net
