In fullscreen the game will run at 120fps fine, the correct refresh rate for the monitor, but in windowed mode it only runs at 60fps. If I disable VSync then it runs at thounsands of fps so it's not a case of a lack of performance. I've correctly set the refresh rate in the ModeDescription.
In windowed mode in Windows Vista and Windows 7, as well as OS X and many modern Linux desktop incarnations, the application has zero control over refresh. The application's front buffer is really just another off-screen surface used by a compositing system, like
dwm.exe in Windows, which then composites the final full desktop image. It may run at a different frame rate than you want, and your application's rendering may be limited to that rate (since it has no reason or ability to worry about the monitor's native rate).