I feel like throwing this in here, but I had an account here that had my new email as my long in, and this account as an old email. When I update my WLID on this account to my new email, it prevented me from logging into the other account. Something along those lines could be the cause of confusion.
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This is what I've been suspecting: Behind the scenes, the credentials are ([i]or were at some point[/i]) based on email addresses rather than PUIDs (using PUIDs provided by the Microsoft Account service would allow for users to change the email address rooting the MS Account without deleterious effect on partner websites).