This will probably not work either, as the 6.5 Media server will effectively become the 'client' of the 5.1 media server during the duplication. The format of disk images is changed in 6.5. Your best bet is to log a call with Symantec. I'd be interested to hear what they say.
What is the NBU version on your netware servers? No matter what the version of the media server, you will only be able to backup clients on 5.x. See 'NetBackup backward compatibility' in the NetBackup 6.5 Release Impact Bulletin:
http://seer.entsupport.symantec.com/docs/288210.htm