I investigated your project. I hadn't got your idea right from the first post. Now with the project it is all clear. The problem is that RadWindow is a pop-up so there is no way to see a UserControl above it, as it always will be on top.
You can do two things, one is to hide the window in order for the message from your project to be seen and after it fades the window to show again. The other is to put the UserControl in a pop-up or in another RadWindow. I am not preparing an application because I don't know exactly what are you truing to do, but if you need more help or sample project I will be glad to help.
the Telerik team