Answer: This can happen if the MSI that was used to install EndNote was on a CD or removable drive, if EndNote was installed by a customized installer, or if a cleaning utility removed install files.

A Windows Installer CleanUp Utility provided my Microsoft has proven useful in some cases.

Microsoft has this utility here:

http://support.microsoft.com/default.aspx?scid=kb;en-us;290301

That allows you to remove the MSI information from windows.

Run this utility, and remove EndNote (remove all found instances).

This will remove the program from add/remove programs for all users.

Installing from the original installer should then work, and allow you to Upgrade/Patch/Uninstall properly.