I got this error yesterday while running FxCop application from Microsoft. I think the problem was because of the .Net framework installed on my machine, I have only .Net 4.0 installed and no other versions of .Net. And I think FxCop was expecting .Net 2.0 in the system.
After few searches I found the resolution for this issue. You can add supportedRuntime tag to the application config (It will be like ApplicationName.exe.config in the same folder where application installed.) file, under startup tag, and set the attribute of the supportedRuntime as the version of the .Net Framework installed in the system.
<startup> <supportedRuntime version="v4.0.30319" /> </startup>