We have a mixed mode assembly application (MFC+WinForms) running on .Net 4, Windows 2008 R2 that constantly uses 100% cpu on one thread.
Using ProcessExplorer we see
You might consider using the profiling tools in visual studio to identify hotspots in your code that could be contributing to this problem. To get symbol support for the .net CLR see this link.
http://blogs.msdn.com/b/sburke/archive/2008/01/16/configuring-visual-studio-to-debug-net-framework-source-code.aspx