I've done a bunch of web searches and found tantalizingly close suggestions on how to fix the "multiple entries in install/uninstall" problem after upgrade.
To summarize what I have double checked:
1) Product codes are different.
2) Upgrade codes are the same.
3) It is a MAJOR upgrade
From the MSI log:
The upgrade does shutdown the running application and installs the new one, starts, etc.
As far as everyone is concerned the upgrade was successful. The only baggage is that there are two entries in the add remove (install/uninstall) system applet. Since the upgrade is in-place, removing either one removes the installed software; and trying to remove the second fails with an error (obviously it has been removed) -- and the second entry is in the applet is removed.
I'm willing to take on an experiment with anyone's suggestion on how to make the upgrade remove the older entry.
If any one needs any more information I'll be happy to supply it.