I cannot exactly reproduce the issue you are facing. One suggestion is to center the window by attaching OnClientShow event to your WindowManager and position the window using the property sender.center(). Give a try with the following approach.
Javascript:
<script type="text/javascript">
functionOnClientShow(sender)
{
varwindow = sender;
sender.center();
}
</script>
Also check the following help documentation which explains more about this. Client-Side Events.
This usually happens due to a problematic CSS setting on the page - e.g. position:relative to a parent element, which breaks the CSS of the control. If examine the screenshot in the original post, the modal dialog does not cover the whole page - this indicates that there is a CSS issue on that page. To be able to help however, we need to get either a live Url or a sample project that reproduces the problem, so we can examine it closely.