Hi Marek,
You have couple issues here:
1. Per the latest "NetBackup 5.x Operating System Compatibility (updated July 16 2007)", NetBackup 5.1 does not support Windows 2008 client. As a matter of fact, Windows 2008 client was not supported until NBU 6.5.2 - follow link below to see that in "NetBackup (tm) 6.x Operating System Compatibility List (Updated April 22, 2009)"
http://seer.entsupport.symantec.com/docs/278064.htm
2. The End of Standard Support for NetBackup 5.1 was March 31st 2008 and the End of Support Life is December 1st 2008. This has been officially announced a while ago.
So I guess you installed NetBackup 5.1 (probably w/ MP7) client on the Windows 2003 machine? The backup may work, but there is no guarantee since it's not officially supported in NetBackup 5.1.
I'd suggest you either upgrade to 6.5.3.1 (6.5.2 at least), or try configure the backup policy with drives or directories explicitly listed in the "Backup Selections" list.