Little bug in the lastest Skype release: the "mark all as read" button for history doesn't seem to work correctly. More accurately, there seems to be "ghost events" that are not visible but are still marked up as "new".
In effect, that means that Skype currently tells me there is one new event in the queue, while there is none.

Restarting Skype clears up the problem.

Do you mean that tray icon remains to say that there is new event?

Both the tray icon and the history button (on the right of the available credit) remained.
This bug might be hard to reproduce: since I installed Skype beta, I've only seen it once.