I don't know what happend, I can't see skype in "startup" tab on task manager The option in enabled in skype settingstry reinstalling it, or check whether an update is pending under store, also tell us does this begin instantaneously?
My computer doesn't give me any problems whit Skype except when it crashes. But try reinstalling it or updating it. If that doesn't work try disabling the automatic startup and re enabling it. Hopefully the futur Windows 10 updates help. Good luck.