Have a windows 2003 domain with one domain controller that is a Windows 2003 R2 64 machine. I tried adding a 2008 r2 domain controller, did the ADPrep for forest, domain, gpprep. When I do the DCpromo on the 2008 server it seems to go through the setup without issues, but it does not create the SYSVOL or Netlogon share. Also if I shutdown the 2003 DC users can not authenticate. I've done this a couple other domains and don't think I've missed anything. Only difference on this domain is the Pre WIndows 2000 domain name is different than the current domain name. Pre Windows domain is domain, while the 2003 AD name is domain1.com.
I didn't set this domain up so maybe something else is goofy just not sure where to look.