If Skype is starting up every time you log in to Windows, it may have been set to do so by default. If you want to prevent Skype from starting up automatically, you can modify its settings so that it will only start when you tell it to. You can also disable its pop-up system tray notifications or modify what actions you receive notifications for.

Disable Automatic Startup

Click "Tools," then click "Options." Under the General Settings category, uncheck the box for "Start Skype when I start Windows," and then click "Save." This will ensure that Skype starts only when you manually open it yourself.

Disable Notifications

Notifications are the pop-up windows that show up by default in the lower right corner of your screen when you get a call, a contact comes online and various other actions. Click "Tools," and then click "Options." Click "Notifications" in the sidebar, and then look through the different options. If you want to disable all notifications, uncheck all the boxes. Click "Save" when you are finished.