msconfig is a diagnostic utility. It is not meant to be used for permanent disabling of the startup items.
The best way to disable a startup item is to do it through the options of the utility itself.
If the program does not provide the option of disabling its startup with windows, there are registry editing programs that let you do that.
Anyway, if you want you can download msconfig for win 2000. Search for it. This is one example:
http://windows.about.com/od/tipsarchive/l/bltip475.htm