How did you deploy the upgrade and was 2003 upgraded at the same time (and before or after endnote - as it needs to be after?)
Did you upgrade from a previous version of Endnote? Which version? In our experience, upgrading from X (and maybe X1) to a later version often leaves behind old toolbars or links to the old program that causes problems. X was installed in user folders which are often not cleanned up, unless the individual user is performing the uninstall. X2 and later versions install in “all user” folders and the upgrade process goes much smoother. If this is your problem, reply, and I will dig out the clean up procedures our IT people employed.