Skype can be a pain, with the constant notifications in the Hub, and it doesn't seem to play well with Contacts, as you've pointed out. Under the Skype settings, you can tap "Sync Contact" and choose the option "Don't share my Skype contacts with other applications". This seems to have taken care of it for me. Also, since I don't like the constant Skype notification in the Hub, I sign out whenever I'm not planning to use it.
12-11-13 07:01 AM