I think that Setup.exe is created by default. If you want to generate an .msi file but not a Setup.exe file, you'll want to configure the Setup Launcher setting accordingly. So, in the Releases view, select the release type that you are building. Then, on the Setup.exe tab, change the value of the Setup Launcher setting.
I am seeing the same issue Bill I have turned off the exe selection on the build step, selected msi, and it is generating an exe with a msi in it. not a straight msi. have you found a solve for this yet?
It sounds like you are using the product in eval mode. In eval mode, InstallShield generates only compressed Setup.exe files; it does not generate other types such as .msi files, regardless of which release settings you select.
