Andrew,
Where is this "NET 4.0 is not installed" message coming from? Did you add it (e.g. in the script)?
Or did you accidentally mark the ".NET Framework is Installed" System Software Requirements that checks if .NET4 (or whetever) is installed and if this is not the case, aborts the install?
"The Requirements Visualizer allows you to specify certain machine environments that your application requires in order to run properly. If these system requirements are not met, the installation will exit. Because your application cannot be installed on systems that do not meet your hardware or software requirements, you may want to set those requirements liberally."
Friedrich