The RadWindow renders as a direct child of the form element so that it can pop up above all else and not be affected by their styles. If we left it where it was declared many issues with the popup behavior would arise.
I am not sure how exactly your styles are inherited and what I can suggest at this point is adding a class for the controls in the RadWindow both in the CSS and in their own declaration, or cascading the existing ones through the RadWindow CSS class if necessary. You could also put a div element in the RadWIndow's ContentTemplate to act as a parent for your controls, that div could have the correct CssClass property like it would be in the markup so that your controls can still inherit the CSS cascade.
the Telerik team