Hi Andy,
According to the error message "The Windows Integrated Authentication endpoint is missing from the Metadata Exchange (MEX) document that is published by the federation server", this issue may occur if the windowstransport and usernamemixed service endpoints are disabled in the on-premises AD FS Federation service.
have you tested the solutions in the article which I provided in the old thread: http://support.microsoft.com/kb/2707356 ?
I understand that you have run the Office 365 Single Sign-On Test on Microsoft Remote Connectivity Analyzer. If possible, please re-run the test and click Expand All option, copy all the test details and provide the information for further troubleshooting. To protect customer's sensitive information, you can provide it via private message (PM).
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Thanks,
Bourne Zhang
