>It seems that removal happens prematurely. If I have one or more of those messages (word searching) and click on Agent icon (which has count > 0), there're no messages there. I still see them in the Subscriptions panel though.

It seems the refresh probably didn't made its loop. The refresh is at two minutes minimum. So, it could be that the messages are still shown on the right side but on the next refresh, they would go away. So, if you click on the Agent during that time, this could be a representation that is in fact normal.