The only way I can imagine that happening is if you have multiple notifications, and you think you are updating the correct one, but in reality you are updating the wrong notification. One test might be to turn off the notification (temporarily) and then trigger it. If the notification still fires, you are working on the wrong notification.
Other than that, you can look at the single record message and multiple record message to see if you need to update both - but typically the multiple record notification is really different than the single and you would notice that, but worth a look.
If neither of those options work, perhaps a customer support ticket is in order.