A number of people have reported problems with the Packaging and Deployment Wizard under Windows 2000. The good news is that some of these errors have been corrected via the Visual Studio Service Pack. The current service pack for VS is SP 4, and it's available at this URL:
<a href="http://msdn.microsoft.com/vbasic">http://msdn.microsoft.com/vbasic</a>
I'd recommend at least checking out what SP4 fixes…it might take care of the problems you are having.