Which NetBackup version?
Great idea to migrate to W2008 X64. Our in-house master server is W2008 - not a single problem.
Just confirm compatibility and ensure you have the 64-bit installation:
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
Note: This CD also contains the x64 Java console and uses VSS as the default option for Windows Open File Backup (WOFB).
Compatibility:
NBU 6.5: ftp://exftpp.symantec.com/pub/support/products/NetBackup_Enterprise_Server/325328.pdf
NBU 7: ftp://exftpp.symantec.com/pub/support/products/NetBackup_Enterprise_Server/337048.pdf
Using catalog backup and recovery to transfer NetBackup catalogs between Windows master servers as part of a hardware refresh
http://seer.entsupport.symantec.com/docs/337969.htm
And read all the TechNotes regarding W2008 installations, e.g:
http://seer.entsupport.symantec.com/docs/318040.htm
(there are more TechNotes, just Google them..)