I'm backing up SharePoint 2001 servers with NBU6.0MP1, but not w/out some struggles. First I called tech support, but by the time they got me an answer I was calling them back with the answer! What errors are you getting?
Anyhow, the catch to ours was taking that ID that has access to the SP database and rather than running the service on the local SharePoint machine as that account, bring that account information back into the NBU client properties screen under the SharePoint 2003 options (Client Properties-->Windows Client-->SharePoint 2003). Then you can set the client service back to running as the Local System account.
Not knowing your error, this is all the advice I can give right now. We personally are struggling with the scheduling piece of the backup. If I kick them off manually, they work like a charm. If I let the schedule initiate the job, I get error 69. Let me know if this helps!