In WPF all Popups are shown at the top of the application above all windows and MessageBoxes. RadDocking's AutoHide
area is a Popup and when it is visible and you try to open Window, it is placed behind the Popup. Unfortunately we cannot do anything to reorder the positions, this is a Framework behavior. The only workaround is to use a new Popup for your confirmation dialog instead of using MessageBox or Window. This Popup will be shown on the top of the AutoHide
We are really sorry for the caused inconvenience. Feel free to contact us in case you have any problems or concerns.
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