Also make sure the new 2012 R2 domain controller is up to date too, as there is an important fix in one of the update rollups related to 2003 compatibility.
AFAIK it is because this patch shipped with the same version of win32k. If you look at the KB article you will see a list of patches that shipped with the buggy version of win32k that had to be...
Yea, this is just a return to what NT4/2000 custom support used to cost back in the day.
I think the original KB article said it would be added.
Chad has written about how to import them into WSUS: http://chadstech.net/microsoft-csa-patches/