I am sorry I did not explain this change in more details.
We remade big part of RadWindow for Q2 2011 and decided that this is the correct way to do things. Previously when RadWindow was declared in XAML we were removing it from its Parent and put it in a popup then show it. Clients tend to bind elements in the window to another XAML element and this binding getting broken and there were also other problems like panels layout being refreshed because of removing the window etc...
We believe that it is better practice to either create RadWindow in code behind or use it as a root element of a UserControl.
the Telerik team