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Possibly a bad vpd.Go to this location and rename the Gen1 folder:$J(user.home)/InstallShield/Universal/common Reinstall the project, this will recreate the Gen1 folder. Then uninstall and see if you get the same behavior.
Why don't you switch to the new user prior to running the installer? ISMP can create/delete accounts, but I don't think it can switch to a new user account.
If you have two different projects but one vpd, you can use the getSoftwareObject method in the RegistryService. It doesn't matter what project the assembly is in. They all get written to the same vpd.But if you have two vpds for the two projects, ...
Under sequences of the second assembly project, are the panels that you want to be displayed inserted under Assembly Sequences? Only these panels will be shown when you run the universla installer.