It was really frustrating. With Windows Phone 7.8 my OneNote synced perfectly fine with SharePoint 2013. Now I have a new Windows Phone 8, but OneNote synced only the sections and then gives an error (e4010647) and shows "Never synced".
Ok, I couldn't find any solution on the Internet, but after some testing with authentication settings I got it: My SharePoint WebApp has "Anonymous access" enabled. However the site collection itself does not allow anonymous access. After modifying the "Authentication Provider" and disabled "Anonymous access" everything is back to normal.
Why? I have no idea…