A common issue i have found with the Windows Live Messenger 
on Windows 7 is that it does with the system tray and remain working from the Taskbar.
However here is a simple workaround that gets it back to the System Tray.
1) Close all intenses of Windows Live Messenger.
2) Go to the Start Menu > All Programs > Windows Live > Right-Click on Windows Live Messenger. Select Properties.
3) Under the Compatibilty tab, tick Run this program in compatibility mode for: Windows Vista SP2. Then click OK.
4) Open up Windows Live Messenger. It should now be running from the System Tray.
Really thank you so much for this information as i was really upset to fix this. 🙂
These tips are very simple and useful. Thank you for sharing with us. Keep up the good works.
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