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It looks like the Make VS.NET action does not honor that option when modifying the project file (just AssemblyInfo. or .RC files). We'll put this on the list to fix for a future release. A couple of workarounds:
1) Checkin the .csproj files after the build has set the base address (this is the only option that would cause the Make VS.NET action to modify the project file, and the action won't modify the .csproj file on subsequent builds if the base address is already set). It's recommended that you check in any source changes made by the build into source control anyway.
2) Don't use the Set Base Address option for the project.
3) Change the 'Handing of writeable local files' option on the SourceSafe action to Replace.
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