O que pode estar acontecendo é que você está usando o CD com a ferramenta 64 bits do adprep.
Ao tentar rodar o ADPREP /FORESTPREP de um CD Windows Server 2008 R2 x64, a seguinte mensagem poderá aparecer.
C:\support\adprep>adprep /forestprep
The image file C:\support\adprep\adprep.exe is valid, but is for a machine type other than the current machine
Isso acontece porque você está rodando a versão x64 em um DC 2003 x86, você deve localizar a versão 32 bits do ADPREP e rodar novamente.
C:\support\adprep>adprep32.exe /forestprep
ADPREP WARNING:
Before running adprep, all Windows 2000 Active Directory Domain Controllers in the forest should be upgraded to Windows 2000 Service Pack 4 (SP4) or later.
[User Action]
If ALL your existing Windows 2000 Active Directory Domain Controllers meet this requirement, type C and then press ENTER to continue. Otherwise, type any other key and press ENTER to quit.
c
Opened Connection to SRVDC01
SSPI Bind succeeded
Current Schema Version is 30
Upgrading schema to version 47
Connecting to “SRVDC01″
Logging in as current user using SSPI
Importing directory from file “C:\WINDOWS\system32\sch31.ldf”
Loading entries……………………………………………………….
Agora é só aguardar carregar tudo e pronto.
[]s
Tiago Souza
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