Like I did recently, I've noted several other users run into a problem where the mod shows Notifications of threads to moderate but when you click on the Notifications dropdown menu, there are no threads to moderate, etc.
What I've done to clear those messages is to totally clear out the moderation table with a simple mysql query:
This will nuke all moderation messages in that table so don't use it unless that is your intention.
Hope that helps. -- Rik