OneNote can have permission issues when synching with Microsoft Office 365 online. The error message I received was: Permission Required.
On research I found that I actually had OneNote for Windows 10 installed and not OneNote that comes as part of the Office suite. If you are in the same situation then simply uninstall the OneNote for Windows 10 app and reinstall/modify the office installation. Once you re-login then the issue should be resolved.