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The msi's for EndNote don't include all the custom actions for doing upgrades, so even if you add in upgrade codes you would still need to add in these actions, which isn't trivial.
Use MSI file from CD. Remove the Palm features and the EnX.msi package is ready for deployment thru Group Policy, on Win XP with Office2003. It is recommended to uninstall earlier versions prior to this deployment.
Virtualization with App-V 4.6.x of Endnote X401 on W7x64 hangs during installation on "Export Helper". Issue solved by sequencing with App-V 4.6.0 on WinXPsp3