Hi,
It sounds as though rather than use a window using a switchto frame could be needed in this case. If the window is within the webpage usually these are iframes or alerts. In my experience this is usually dealt with by the SwitchTo().Frame API method, I normally supply the iframe title to switch focus. I hope this is resolved and is of some help. Let me know if not and we can work on this I'm sure as deal with multiple windows / iframes / popups daily across my QA platform and they're interesting to work with,
driver.SwitchTo().Frame(<This has 3 overrides>);
Cheers
Sean