Does Active Directory on Server 2003 R2 support IPv6 subnets in Sites and Services?
You'll need to upgrade the schema of your Active Directory in order to have support for IPv6 subnets. Running the adprep utility from Windows Server 2008 (or R2) will be sufficient to upgrade your schema to a version that supports the new IPv6 subnet objects.
It turns out that Windows 2003 Domain Controllers will not accept IPv6 subnets in Sites and Services. After adding a 2008 R2 domain controller, I was able to add IPv6 subnets. But I also found out that running IPv6 on Windows 2003 does not work out very well, especially with Exchange in the mix.