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I found another potential source. If FxCop can't find all your assemblies, it will throw warnings and mark the build as unstable.
http://stackoverflow.com/questions/12120741/code-analysis-error-could-not-load-file-or-assembly-system-net-http-version-2
You can tell fxcop to scan the global assembly cache (/gac flag), or sometimes you need to change the FxCopCmd.exe.config file to change it's assembly lookup strategy. On a different project than the one above I had this error in my output:
I had to change FxCopCmd.exe.config to set