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Try specifying the full v4.0 version number in the supportedRuntime setting (for example, version="v4.0.30319").
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My suggestion is to provide more information. Are you using DirectX? I am not as knowledgeable as others are on this subject but I can at least suggest what you should provide to assist others to assist you.
The best solution is to determine what is using version 'v2.0.50727' of the runtime and either re-build it using version 4 or get a newer version of the software that uses version 4 of .Net. Do you at least know what it is that is using version 'v2.0.50727'? If not then perhaps someone can explain how to determine that.