ASP.NET ModalPopupExtender appears when calling Alert JavaScript function - asp.net

Question

I'm facing a buggy behavior from ASP.NET Ajax Controls Toolkit ModalPopupExtender, when I call Alert() JavaScript function from server-side the modal appears in the back ground. I don't know why this is happens.
here is the code:
vb:
Sub ShowAlert(ByVal message As String)
ScriptManager.RegisterStartupScript(Me.UpdatePanel, UpdatePanel.GetType(), "notificationScript", "<script language='JavaScript'> alert('" & message & "'); </script>", False)
End Sub
aspx:
<asp:UpdatePanel ID="UpdatePanel" runat="server">
<ContentTemplate>
<asp:Panel ID="pnlPartialInstructions" CssClass="modal" runat="server">
......
<asp:Panel ID="pnlPrintConfirmation" CssClass="modal" runat="server">
<table class="ui-accordion">
<tr>
<td colspan="2">
<asp:Label Text="Do you want to print the receipt?" ID="lblPrintConfirmation" runat="server"
meta:resourcekey="lblPrintConfirmationResource1" Font-Bold="True" Font-Names="tahoma"
Font-Size="Large" />
</td>
</tr>
<tr>
<td>
<asp:Button ID="btnConfirmPrint" Text="Yes" CssClass="google-button google-button-blue"
runat="server" meta:resourcekey="btnConfirmSaveResource1" Font-Size="Large" />
</td>
<td>
<asp:Button ID="btnCancelPrint" Text="No" CssClass="google-button google-button-red"
runat="server" meta:resourcekey="btnCancelSaveResource1" Font-Size="Large" />
</td>
</tr>
</table>
</asp:Panel>
<asp:Button ID="HiddenForModel1" Text="" runat="server" CssClass="hide" CausesValidation="False" />
<ajaxToolkit:ModalPopupExtender ID="pnlPrintConfirmation_ModalPopupExtender" runat="server" DynamicServicePath=""
Enabled="True" TargetControlID="HiddenForModel1" PopupControlID="pnlPrintConfirmation"
BackgroundCssClass="ModalBackground" DropShadow="True" CancelControlID="btnCancelPrint"
RepositionMode="RepositionOnWindowResizeAndScroll">
</ajaxToolkit:ModalPopupExtender>
.....
</asp:UpdatePanel>
</ContentTemplate>

Answer 1

The issue is caused by the way the ModalPopupExtender works. It is emitting a JavaScript which will hide the Panel.
Now you are registering your alert() call as startup script, this will hold running the ModalPopupExtender script as long as the user will not exit the alert windown. The simplest fix is setting display:none on the Panel so it will not need the script to hide it:
<asp:Panel ID="pnlPrintConfirmation" CssClass="modal" Style="display:none;" runat="server">
...
</asp:Panel>