To be more precise I had a customer running CRM 2011 IFD with ADFS.
CRM server was in domainx.local and users and ADFS server were in domainy.local
Created users in CRM with Username firstname.lastname@example.org and email@example.com etc...
The customer wanted a Development Organization copy (crmdev) from their current production environment (crm)
So I backed up the production database (crm_mscrm) and restored it to an alternate database (crmdev_mscrm)
So then I fired up he Deployment Manger and ran the Import Organization and kept the User Mappings (user1 -> firstname.lastname@example.org and user2 -> email@example.com) and the import was succesfull.
After the import I logged in as the System Administrator and all worked out OK.
But then I wanted to login as an alternate (normal CRM user) firstname.lastname@example.org I faced the dreadfull 404 not found error.
Logging in as another user (email@example.com) also gave me a 404 not found error.
So time to start digging around...
Solution was quite stupid i changed firstname.lastname@example.org to email@example.com and then back to firstname.lastname@example.org and then I was able to login succesfull
Did the same for email@example.com -> firstname.lastname@example.org -> email@example.com and tada same succes.
So if you restore a production CRM organization (with ADFS and ADFS users/UPN) on the same CRM serveras an extra tenant/organization be sure to change the USERNAME for all the users in CRM to some blabla and then back to their original UPN.