Here is an example of the problem that I am talking about Skype Minimized to Windows 7 Taskbar, not on the System Tray
But now I will show you how to Minimize Skype to Windows 7 Syatem tray / Notification Area
Go to Tools > Options
Select the Advanced tab
Now Uncheck the option that says “Keep Skype in the task while I’m signed in“.
Press the Save button. And from now on Skype will be Minimized on the Windows 7 System Tray rather than the Taskbar.
To Minimize Skype to Windows 7 System Tray you will need to press the Close button. Press the Minimizing button will minimize Skype to the taskbar and press the Minimize button will Minimize Skype to Windows 7 System Tray.