The problem with the DragEnded event is that RadTreeView has a delay on its drag and drop that exceeds the default Dispatcher.BeginInvoke
and then the focus is again taken by RadWindow. Therefore, if you delay a bit more showing the Confirm window it is working fine. Here we can do nothing, because of the drag and drop implementation, whose delay can't be reduced.
About the first issue, It appeared that in Silverlight 3 Microsoft have introduced some changes related to focus of pop-ups and this is breaking our implementation of RadWindow. It appears that RadWindow is not gaining focus. You can modify your project and put a Button in the second window. If you focus the Button, before switching to another application it is working properly. We are now discussing how to change our implementation and will try to resolve this problem for SP1.
For now as a workaround you can set manually focus to an element in the second window after showing it. Thank you for your time and detailed examples. We will do our best to fix this focus issues. I have updated your account with 1000 Telerik points.
the Telerik team