When trying to bring another DC online to active directory via DCPromo I kept getting an error message telling me to run forest and domainprep even though I had already done so.

Before you can introduce Windows Server 2003 domain controllers, you must prepare the forest and domains with the ADPrep utility.

ADPrep /forestprep on the schema master in your Windows 2000 forest.
 
ADPrep /domainprep on the Infrastructure Master in each AD domain.

After some digging I found there was a different (and slightly larger version) of Adprep knocking around on CD2 of Windows 2003 R2

It's in:

CMPNENTS\R2\ADPREP

After running the above usual adprep syntax using this file the new server could then successfully execute dcpromo as expected.