Recently I have run into multiple issues with IPv6 enabled on Windows Server 2008 and simply de-selecting the protocol on the network interface card in Windows does not fully remove the functionality. Previously the need to use regedit was required to fully disable the protocol and while this is still the case, Microsoft has released a tool that automatically does this for you. The best part - a reboot is not required and typos are eliminated!
A Microsoft Knowledge Base (KB) article describes the process or a direct link to the download is listed here http://go.microsoft.com/?linkid=9646967. Failing to fully disable the protocol will cause communication issues specifically in Microsoft Exchange 2007 and beyond (http://support.microsoft.com/default.aspx/kb/952842).