Hi,
You can do two things,
First, you can get the divCommentsMsg div by following way and fade it out:
$("#<%# divCommentsMsg.CliendID %>").delay(3000).fadeOut(100);
Second, you can get that div by its class. Make sure class of that div is not used anywhere else.
$(".form_popup_Msg").delay(3000).fadeOut(100);
I hope this will help.
Thanks :)