Consider the following scenario:
You sign in to a Microsoft Lync 2010 Group Chat client, and then you join a chat room.
You click the Actions menu, click Notification…, select the Show alert and the Flash button on the taskbar options, and then you click the OK button.
You click the Connect menu, click Preferences…, select the General tab, select Minimize to the notification area option under When closing the main window, and then you click the OK button.
You select and focus on the chat room, and then you click the close button to minimize the window.
Another user joins the chat room and sends a message.
In this scenario, you do not receive a new message indicator for the message to the chat room.
To resolve this issue, install the following cumulative update:
2636065 Description of the cumulative update for Lync 2010 Group Chat client: November 2011