Interesting information here. Not sure if it applies to a Server 2008 AD but if true I'm sure it probably does a 2003 AD.

Cross-Forest trusts

NetBIOS is still used in the trust creation process. Forests that have the same NetBIOS name for their Forest Root Domains will not be able to create trusts between them, and the only method around that is to re-install one of the forests and to re-create it from scratch.

http://www.petri.co.il/disable_netbios_in_w2k_xp_2003.htm