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Run dcdiag and netdiag from the command prompt on the old machine to check for errors. If you have some solve them first. For these tools you have to install the support\tools\suptools.msi from the 2003 installation disk.
Prepare the current Active Directory forest to accept a Server 2008 R2 DC. You do this by running
Adprep.exe /forestPrep (Adprep32.exe /forestPrep on x86 server)
found on the Server 2008 R2 installation DVD in the Support folder on the current DC.
http://technet.microsoft.com/en-us/library/cc731728%28WS.10%29.aspx