Could you please make sure that you set the Overly property to the right RadWindowManager? I ask you this because if you have two or more RadWIndowManagers on the page (including MasterPages and user controls) then the first one will be used by the global methods like radalert, GetRadWindowManager, etc. If this is not your case, could you please open a new support ticket and send me a sample which shows the problem. I will check it and do my best to provide a working solution as soon as possible.
All the best,
the Telerik team
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