When building an installer in Visual Studio 2008 SP1 and including the bootstrapper installer for .NET Framework 3.5 SP1, you may get 2 warnings when building stating:
Warning 1 The value of the 'PublicKey' attribute in '.NET Framework 3.5' does not match that of file
'C:\Programmi\Microsoft SDKs\Windows\v6.0A\Bootstrapper\Packages\DotNetFX35\dotNetMSP\x86\xxx.msu'.
...
and
Warning 2 The value of the 'PublicKey' attribute in '.NET Framework 3.5' does not match that of file
'C:\Programmi\Microsoft SDKs\Windows\v6.0A\Bootstrapper\Packages\DotNetFX35\dotNetMSP\x64\xxx.msu'.
...
For some reason in the product.xml file for DotNetFX35SP1, the "xxx" files have a different PublicKey than all of the other files in the dotNetFX30 packages for the DotNetFX35SP1 bootstrapper. To fix the issue replace the "xxx" PublicKeys with one of the other keys (they are all the same).