This could happen if RadWindow's object is not destroyed when the window is closed (e.g. DestroyOnClose is set to false). By default this property is set to false and when a RadWindow is closed, it remains hidden on the page - this is done in order to provide a caching feature so the window can be opened immediately when called again.
Please set DestroyOnClose to true - this should help in your scenario. Note however that when DestroyOnClose is set to true, you will not be able to open that same RadWindow again until the whole page is reloaded - a new RadWindow with default settings will be opened instead. That is why it is better to set the needed properties of the window either in the RadWindowManager or with the client-side API.
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