Authentication fails on Windows phone. User GUID is compared to email

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I am developing an Ionic 2 project (built on Cordova) using the Azure Active Directory ADAL plugin for Cordova:

https://github.com/AzureAD/azure-activedirectory-library-for-cordova

It authenticates properly on Android and IOS but fails on Windows Phone 10. I have debugged the problem all the way until the part where it goes into native code and it all seems fine.

I am internal at Microsoft and doing the authentication flow and I am actually first sent to one login screen for our mobile application before being redirected to the org sign-in page which does the two factor authentication flow. After the 2FA flow is accepted it redirects back to our application but then fails because it does a string comparison to compare the login request text to what was returned but fails because the login text is of format [email protected] and the returned identifier is my user GUID. I have verified that this is indeed my unique user GUID but it should not be compared to my email address.

Response

Is there any work around for this issue?

UPDATE: Here is the JWT. Got it from Fiddler. I saved and anonymized some of the request/responses too, let me know if you need them.

{ typ:"JWT", alg:"RS256", x5t:"RrQqu9rydBVRWmcocuXUb2*****", kid:"RrQqu9rydBVRWmcocuXUb2*****", } { aud:"5712d3fd-8e22-4040-afbf-********", iss:"https://sts.windows.net/72f988bf-86f1-41af-91ab-********/", iat:1482954230, nbf:1482954230, exp:1482958130, acr:"1", amr:[ "pwd", "mfa" ], appid:"197e6baa-c9ed-4354-a561-***********", appidacr:"0", e_exp:10800, family_name:"****", given_name:"*******", ipaddr:"167.***.***.***", name:"****** ******", oid:"e9a9b8a5-46e5-4c78-9593-***********", onprem_sid:"S-1-5-21-2127521184-1604012920-1887927527-**********", platf:"14", puid:"10037FFE814B****", scp:"Directory.Read.All Users.Read.All", sub:"Jd7cxiEcj-7uVvBc-O0b8VYsT0GdXz1KDD-*******", tid:"72f988bf-86f1-41af-91ab-********", unique_name:"******@microsoft.com", upn:"******@microsoft.com", ver:"1.0" }

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