If I understand correctly, you load a RadWindow with a NavigateUrl that contains a link to an anchor in the content page, am I right? If this is so, this is a known problem, that however is not directly related to the RadWindow control - you will get the same behavior if you use an IFRAME instead (sample attached). The reason for this behavior is that the browser always tries to focus the anchor and show it on top of the page which leads to the "jumping".
If this is your exact scenario, I would suggest to set ShowContentDuringLoad to false for the RadWindow / RadWindowManager - this way the initial content of the window will be hidden until the page is loaded and the browser will not focus it.
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