I tried testing sending a private link to my server to one of my friends over Skype after reading the first Heise article. To get a response from Skype, I contacted them. I think you might find the following very interesting:

"You are correct, Skype chats and conversations are encrypted. Your chat can only be read when you sign in using your Skype name and password. Not even Skype or Microsoft has access to your chat history. "

You can see the full transcript here: http://pastebin.com/bbiSWtrz