You shouldn't have to configure this manually. What are the values you are using for ConfigurationToBuild (look in your TfsBuild.proj file) Typically the PlatformToBuild value for a web service will need to be .NET, while for other types of projects (e.g. C#) it might be Any CPU or something else. If you have a solution with both a web service project and a C# project, you will typically have a platform called Mixed Platforms - if you specify this platform in TfsBuild.proj everything will typically compile OK.
-Aaron
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