I downloaded Visual Studio 2012 yesterday when it was released on MSDN. I have noticed that a few of the project types that we had in 2010 are gone or different. The bigges
Visual Studio setup projects are back in VS 2013 as a visual studio extension.
https://visualstudiogallery.msdn.microsoft.com/9abe329c-9bba-44a1-be59-0fbf6151054d
Please update your solution and projects to VS 2013. If you are still in VS 2010, you are probably better off by upgrading directly to VS 2013.
My experience with Installsheild LE is that it is very quirky but once you figure out the tricks, it is easier to use. However, I think that the limited edition is a way by Microsoft and Flexera to sell the fully featured edition. In other words, first we pay Microsoft a lot of money for Visual Studio and then their partner (in crime) more for Installsheild. Bad strategy which did not work out since they had to bring back the setup projects in VS 2013.