I believe that you are using a standard project in Developer. This project gives you the capability to use InstallScript for creating a script based setup. However, if you want pure MSI, always choose a basic MSi project.
If you do have standard projects, you can convert them to MSI project by using the following tool as described in the KB section of our support site. Here is the link to the article:
http://support.installshield.com/kb/view.asp?pcode=WIND700E&articleid=Q105871If you cannot access this link search for article: Q105781 or
HOWTO: Converting a Standard Project to a Basic MSI Project
When searching for AdminStudio related KB articles, please search in Developer areas as well.