Any compilation to native code takes time. Because .NET cannot possibly compile all the code to the application at once, all compilation must be done piecemeal and therefore must inevitablty slow the program at some point. But I doubt, too, if this compilation can do the the kinds of optimations that a C++ compiler can do. Even if.NET's gains some advantage with hotspot optimization, a C++ compiler can do almost the same thing prior profile information.
Lastly, I don't think the performance of a pure C++ Win32 app is all that much greater than the .NET Framework. I would honestly not expect anything more than 20% increases in almost any application (3D games being a notable exception). When a .NET application is started, it's compiled to native code and from then on runs native.