Good news! A hot fix for this has been released for this at http://support.microsoft.com/kb/2989971.
The ASKDS team at Microsoft recently published a blog about some authentication issues when you mix 2003 and 2012 R2 domain controllers.
The good news is that they are working on a hotfix for this issue right now, so hopefully will not be an issue for too long. If you are following this post, it will probably be best to go ahead and play Taps and let the old 2003 DC’s rest in peace. Extended support for Windows 2003 will end on July 14 2015.