Michael and I continued this discussion via email, but I didn't post the final solution. If I remember correctly, the problem was that I used different versions of the InstallAware software and registration component. After every upgrade you have to generate a new license EXE.
However, that doesn't sound like what you're running into.
Command line build omits .NET Framework
Re: Command line build omits .NET Framework
I had the same problem when I replaced my build machine from Windows XP to Windows 7 Pro x64.
After some research, I found out that the problem was inside my <project>.mpr file:
..\..\..\..\..\Program Files\InstallAware\InstallAware 6.6\runtimes\checkmsi20.mia
..\..\..\..\..\Program Files\InstallAware\InstallAware 6.6\runtimes\setupmsi20.mia
When I replaced this with
..\..\..\..\..\Program Files\InstallAware (x86)\InstallAware 6.6\runtimes\checkmsi20.mia
..\..\..\..\..\Program Files\InstallAware (x86)\InstallAware 6.6\runtimes\setupmsi20.mia
The problem was fixed.
I'm working with IA v6.6 Studio.
After some research, I found out that the problem was inside my <project>.mpr file:
..\..\..\..\..\Program Files\InstallAware\InstallAware 6.6\runtimes\checkmsi20.mia
..\..\..\..\..\Program Files\InstallAware\InstallAware 6.6\runtimes\setupmsi20.mia
When I replaced this with
..\..\..\..\..\Program Files\InstallAware (x86)\InstallAware 6.6\runtimes\checkmsi20.mia
..\..\..\..\..\Program Files\InstallAware (x86)\InstallAware 6.6\runtimes\setupmsi20.mia
The problem was fixed.
I'm working with IA v6.6 Studio.

