Every now and then Windows starts up with Skype running but not in the system tray.
For the life of me, I don't know why. The only way to then go into Skype is to 'launch' it again, which brings the app into focus and on the Taskbar. But then, since I minimize to the system tray and don't keep it in the Taskbar to save space, it gets lost again :(
It's also a pain opening up the Task Manager just to close Skype. So, the solution, kill skype!
Start -> Run -> powershell -command "ps skype | kill"