I am slowly upgrading my projects from VS2005 to VS2008. I had a puzzling problem with the Setup Projects always requiring the .NET Framework 3.5 even when the Setup Project is targeted to 2.0 and the application it is delivering is using .NET Framework 2.0.
There are several posting on the the internet about solving this problem. It basically requires you to go to View/Editor/Launch Condition and change the .NET Framework to the version you desire. The Project properties for your setup project are a bit misleading when they have no affect on this problem.
Read these posting for more detailed explanations:
http://impressionsoft.blogspot.com/2008/03/visual-studio-2008-setup-project-and.html
http://blogs.msdn.com/cschotte/archive/2007/08/15/vs2008-launch-conditions-and-prerequisites.aspx
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