Thank you for the additional information - I think I know now what is going on :)
Behavior like the one you describe could occur if you have more than 1 RadWindowManager on the page. For example - one in the main page and another in the user control.
In such case, you need to take into consideration the following:
1. All RadWindowManager's functions (radopen, radalert, radconfirm, radprompt, GetRadWindowManager, etc) are always using the first rendered RadWindowManager on the page.
2. Every RadWindowManager "knows" only the RadWindows that are declared in its Windows collection.
This means that if you have a RadWindow2 as a standalone control OR declared in RadWindowManager2, and you use something like radopen(myUrl, "RadWindow2");, radopen will use RadWindowManager1 and will open a new RadWindow with the settings taken from RadWindowManager1. To avoid that problem, when you have multiple managers on a page, you need to get a reference to the correct RadWindowManager first and then call its methods.
var manager = $find("<%= RadWindowManager2.ClientID %>");
the Telerik team