It is somewhat complicated to explain.
Let’s say you have a private conversation with a member and the appropriate topic /t/[topic-name]/[numbers] is open. Now the member will send you a new message in this topic. The green indicator for new private messages (on the Avatar) goes to (1). You directly see the message in the topic, since it is already open. Now you switch to another topic and the green (1) is still there.
It would be nice if this was synchronized.