[quote=joerg]you didn't quit skype, but only closed the window? (sorry, but sounds like that)[/quote]
Yeah, joerg is probably right. Skype abuse close button of the main Skype Window, so instead of closing the application it close the active window.
But the application remain active. Sometimes you can bring it from the task bar, but icon on the task bar can be disabled too, so there is no way to bring Skype back.
To close Skype pemanently just use 'Exit' from the menu.
If you happen to 'close' Skype window, and cannot login, open the console and write:
CODE
killall skype
Should help.