I kept getting the error “Unable to access Azure’s API: The server failed to authenticate the request. Verify that the certificate is valid and is associated with this subscription.” when I tried to link Azure to my Docker Cloud organization. Turns out that the generated “Management Certificate” is for my personal account not the organization. Switching back to my account, I was able to link it.
So I think the issue is: Even if you switched to an organization, the “Download Management Certificate” link always downloads your personal version. But during verification (when saving), it uses a different certificate.