I discussed this with William from the OneNote team at the Ignite Conf. He gave me his email address to send the details, but suprise! His email address is wrong.

This scenario plays itself out with many users a.
• Scenario
o A new OneNote file is created in OneDrive for personal, using the OneNote application on a Windows desktop.
o At a later time, on a new session, the user logs into the Hotmail account that is linked to that OneDrive account.
o He then opens OneNote locally on the desktop, and opens the file created earlier.
o Once opened, the file syncs fine.
o Subsequently, he logs into the enterprise email system with his enterprise credentials. He then uses that credential to access other enterprise resources.
o At some point, he begins to see a conflict with the OneNote sync (see link).
o If he clicks on the OneNote needs password…link, he gets an authentication window.
o That window is defaulting to the enterprise credential
o Even if you try to enter your Hotmail credentials, the window keeps on popping up and the sync does not work anymore.

Any help would be appreciated.