To get the RadWindow to center properly, you need to use its OnClientAutoSizeEnd event and  call its center() method:

This issue affects only the Q1 2016 SP1 release.

		<script>
			function OnClientAutoSizeEnd(sender, args) {
				sender.center();
			}
		</script>
		<telerik:RadWindow ID="RadWindow1" runat="server" OpenerElementID="Button1" AutoSize="true" Modal="true" OnClientAutoSizeEnd="OnClientAutoSizeEnd">
			<ContentTemplate>
				<div style="width: 600px; height: 400px; background: yellow;">dummy content for autosizing</div>
			</ContentTemplate>
		</telerik:RadWindow>
		<asp:Button ID="Button1" Text="open RW" runat="server" />