When you say you have two operating systems, I take it that you have two choices to boot from, and can boot to either the old or the new! It sounds to me like when you reinstalled, you didn't chose to use the drive/folder as the previous install. Are both installations on the same drive or did you choose another drive for the new install?
You didn't necessarily need to format, in order to wipe out the previous installation, but in order to overwrite your previous install, you needed to use the same drive and folder. In any case, you can eliminate the previous install by editing the "Boot.ini" file and deleting the directory that contains your previous install.
You need to, of course, be careful of what you delete (that you are deleting the old and not the new), but I assume your previous install was to c:\winnt.
Make sure that indeed you have two separate directories for your OS. It is possible to have two separate entries in the boot.ini, when in fact you have only one set of installation files.
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