Why would a modalpopup appear centered except when prompted by a AsyncFileUpload control

I have a modalpopup that appears whenever there is processing running on a page.

In the MasterPage

<div id="Progress_Update_Animation" ><asp:Panel runat="server" ID="Panel_ProgressUpdate" BackColor="#515151" CssClass="panel_progress" ><table width="100%" cellpadding="30px"><tr><td align="center" valign="middle"><img alt="" src="<%= Page.ResolveUrl("~")%>img/ajax-loader.gif" class="center" /><br /><center><b>Working, ..... please wait</b></center></td></tr></table></asp:Panel><asp:RoundedCornersExtender ID="RoundedCornersExtender_ProgressUpdate" runat="server"
		TargetControlID="Panel_ProgressUpdate"
		Radius="8" 
		Corners="All" ></asp:RoundedCornersExtender><asp:ModalPopupExtender ID="ModalPopupExtender_ProgressUpdate" runat="server"
		DynamicServicePath="" Enabled="True" 
		PopupControlID="Panel_ProgressUpdate" 
		TargetControlID="Panel_ProgressUpdate" 
		BackgroundCssClass="modalPopUpBackground2"></asp:ModalPopupExtender><script language="javascript" type="text/javascript">
	    Sys.Net.WebRequestManager.add_invokingRequest(Loadpopup);
	    Sys.Net.WebRequestManager.add_completedRequest(unLoadpopup);
	    function Loadpopup(sender, args) {$find('<%=ModalPopupExtender_ProgressUpdate.ClientID %>').show();
	    }
	    function unLoadpopup(sender, args) {$find('<%=ModalPopupExtender_ProgressUpdate.ClientID %>').hide();
	    }
	    function pageUnload() {
	        Sys.Net.WebRequestManager.remove_invokingRequest(Loadpopup);
	        Sys.Net.WebRequestManager.remove_completedRequest(unLoadpopup);
	    }</script></div>

This works fine in all content pages except when I am in the Browse windows of the AsyncFileUpload control. The control is in a modalpopup which encloses a Wizard. On the last page of the Wizard is a AsyncFileUploadcontrol. BTW the modal appears correctly on all button clicks of the Wizard. Now after selecting a file (and clicking Ok) from the AsyncFileUpload control browse window, the modal appears, but it isnot centered like everywhere else, it appears to align itself below and to the right of the AsyncFileUpload control Browse button.

Can anyone explain this?

I have tried setting different z-indexes on both but it no difference. The more i use asp, the more i think I should look into other web languages.