Microsoft has just updated the following KB Article:
Active Directory discovery creates computer names that use the domain NetBIOS name in System Center 2012 R2 Configuration Manager
Symptoms:
Consider the following scenario:
- You run a computer that is a member of a domain (such as Domain A).
- The first common name (CN) of the domain fully qualified domain name (FQDN) is different from the domain NetBIOS name.
- The computer is a member of a group in a different domain (such as Domain B).
- Active Directory discovery is run in Domain B in Microsoft System Center 2012 R2 Configuration Manager. In this case, the computer that is a member of Domain A is a foreign security principal.
In this scenario, the computer that is a member of Domain A and all other computers in Domain A are discovered incorrectly as using the NetBIOS name of the first CN of the FQDN of Domain A.
Full details at:
http://support.microsoft.com/kb/2962909