Modal Popup does not work with ScriptManager.RegisterStartupScript for this i created one more modal pop up and kept label blank as i can able to give any message:
<cc1:modalpopupextender id="mdlInfo" runat="server" okcontrolid="btnInfoYes" cancelcontrolid="btnInfoNo" dropshadow="false" repositionmode="RepositionOnWindowScroll" targetcontrolid="btnInfoTarget" behaviorid="programmaticModal" backgroundcssclass="modalBackground1" popupcontrolid="pnlInfo" xmlns:cc1="#unknown">
</cc1:modalpopupextender>
<asp:panel id="pnlInfo" runat="server" style="display:none" cssclass=" ui-dialog ui-widget ui-widget-content ui-corner-all ui-draggable ui-resizable colored-popup" xmlns:asp="#unknown">
<div id="div1" runat="server">
<span>Message</span><a id="A2" class="ui-dialog-titlebar-close ui-corner-all" role="button"><span></span></a></div>
<br />
<table>
<tr>
<td align="center">
<asp:label id="lblInfo" runat="server" text=""></asp:label>
</td>
</tr>
<tr>
<td align="center">
<asp:button id="btnOK" runat="server" text="OK" cssclass="blue-button-thirty-three" onclientclick=" return HidePopup();" />
</td>
</tr>
</table>
</asp:panel>
and ok button hide the modal pop
function HidePopup() {
$find("programmaticModal").hide();
return false;
}