We had noticed in our organization, that after the apps OneNote, OneDrive, etc. were updated they could no longer connect to our office 365 environment. We discovered that the apps changed their method of authentication. We had to modify our ADFS environment to accept Forms based authentication and place it in priority above basic auth. This was done in the Web.config on the ADFS boxes. After we made that change the apps were able to successfully log in. I'm not sure that this will help but i wanted to share our experience in case you are still having similar issues.
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