I have a setup project in .NET. When I save the project and the other projects to subversion, the setup project no longer compiles. I get the error "Unable to update dependencies of the project."
There is a long discussion thread about this on MSDN. It seems like there are many possible causes. The discussion includes a few links for this problem from Microsoft. Here is a hotfix for VS2005 and here is a workaround for VS2010.