Azure AAD Mobile Service Authentication with corporate accounts fails.

Question

I have been having on-going issue with Authenticating against a Windows Azure mobile service with corporate accounts.
Here is the complete environment.
Initially we set up with Office 365 / CRM Online / and Azure for our corporate infrastructure. We have set up single sign on. Everything works well. There is ADFS set up and running to allow us to Authenticate with {username}@{companyDomainName} and everything
works, including single signon. 
Along comes Azure Active directory. We have an Automatically created Azure active directory in the corporate azure account. The domain is the default created {accountname}.onmicrosoft.com domain structure. This is set as the Default directory.
We had a consultant come in, who was organized through Microsoft, to do some work. After everything was set and done we ended up with another active directory created in Azure that is named with the corporate domain name. This second domain has had all of
the corporate accounts synched to it. 
I have now created an Azure Mobile Service. The service is a basic service, I haven't updated any of the code yet, except to publish the service. I have followed all of the configuration instructions for setting up the authentication. 
If configure the Authentication to point at the first active directory, I am able to Authenticate against the service using the credentials for a user that has been created in that domain. The Authentication works correctly, and goes through.
However if I switch the configuration to use the second Active Directory, the one with the corporate accounts synched to it, the authentication fails. I am able to enter my corporate email address into the web page that is presented. Then the web control
started to call into the ADFS in order to authenticate the corporate user name and password. At this point the authentication fails with a message about the service not being available.
The login code is the standard:
user = await App.MobileService.LoginAsync(MobileServiceAuthenticationProvider.WindowsAzureActiveDirectory);
The project is a Universal Application as the service needs to be available from both a phone and a desktop. The project was started from the starter project downloaded form the Mobile Service site.
# Update
I've just switched the mobile service configuration back to use the AAD with the corporate accounts synchronized. The login through the application fails. However if I log in through IE by browsing to : https://{ServiceName}.azure-mobile.net/login/aad
The authentication goes through correctly. 

Answer 1

A few questions on the details:
What client platform are you using for login. In particular, is this a Windows Store application?
What do you mean exactly by "authentication fails?" Does an error get thrown, or does the UI just hang?
Is this being done from a domain-joined machine and/or on a machine connected to a corporate network?
We have seen an issue where some configurations of ADFS will not play nicely with Windows Store apps since the Web Authentication Broker (WAB) is based on the IE browser, and ADFS will attempt to do SSO in the special IE way instead of presenting a form,
etc. Unless the WAB is configured to handle this scenario, you will get a non-responsive UI.
Any details you can provide would be helpful.