Praveen,
Thanks for the response, but that was not it. There are actually Custom Actions that run conditionally based upon the installer being launched from the setup.exe. In order to avoid directly editing the .msi and removing these Custom actions, I simply created an .msi wrapper that launches the setup.exe for Visual Studio. We have tested and this works fine. It seems to be the only solution without editing the .msi directly.
Best regards,
Sophie