I am not certain this is an issue with the RadWindow since the problematic behavior occurs after you perform a certain action in your main page and not when minimizing the RadWindow. You should star off by determining which action is causing the unwanted reaction then inspecting its handlers and behavior.
as this is the JS object that is used to control the URL of the page and to reload it. Please also check the rest of your code for such calls. It is also possible that you are performing some AJAX request that is disposing part of your page. You can easily check this by monitoring the network requests.
the Telerik team
If you want to get updates on new releases, tips and tricks and sneak peeks at our product labs directly from the developers working on the RadControls for ASP.NET AJAX, subscribe to their blog feed