I tried pinning on/off the window, but I didn't noticed any differences in the RadWindow behavior. Is it possible for you to send me a small movie that shows the behavior on your side along with the code that you are using?
In general, the difference between the classic and the ASP.NET AJAX versions of RadWindow is that in the AJAX one, you are moving the RadWindow itself, while in RadWindow for ASP.NET, you are moving a DIV only. When you release the mouse, the object goes behind the applet as expected - in the classic RadWindow however, we are using our own mechanism for detecting that. With RadWindow Prometheus however, we are using the MS AJAX mechanism.
I talked with our Dev team and we manage to come up with custom solution that I hope would fit your requirements. Please check the attached sample and the movie that shows the behavior - you will notice that there are some side effects which are due to the nature of the applet object, but it is the best solution that we can provide.
the Telerik team