Starting from 6.5.4 NBU supports Master Server on W2k8/MSCS.
You will need to download Release Update CD for Windows 2008:
CD Image NB_6.5.4.Winx64_CD.exe provides a media refresh to 6.5.4 for Veritas NetBackup (tm) servers and clients only on Windows 2008 and Windows 2008 Server Core x64 platforms, and for new installs on Windows 2003 x64 platforms
http://support.veritas.com/docs/326387