The other thing that happens is not necessarily system performance related, but operational performance related....
If you put two machines side-by-side, one having been newly installed and one upgraded, you will find several difference in menu options and locations of files that can lead to issues in the future or when you are looking at other problems. For example if you install a new Windows 2000 Server, the user profile information is stored in the Document and Settings folder off of the root of the C-drive (or system drive). However, if you upgrade a machine, it leaves the WinntProfiles folder and profiles in tact. While this really doesn't matter to the machine, to a user trying to find -- say the All Users folder, this could get a little confusing. There are other items like this as well that are embedded in the operation of the machine and the registry.
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