Actually -that happens to me on this site, Moodle.org 
I think it must remember your IP and as I type in my name before I type in my password the message box pops up if I have a message.
Even though I don't have a message the pop-up window comes up? This just started happening after the front page was restored. I think that in the process of restoring the front page it got restored to the wrong course which was merged with the front page. Then restored to the correct page. Could there be something in the messaging system that sees the front page id as being wrong or something and triggering the messaging system? In the front page source before I login I am getting:
<div id="content"><script type="text/javascript"> //<![CDATA[ openpopup('/message/index.php', 'message', 'menubar=0,location=0,scrollbars,status,resizable,width=400,height=500', 0); //]]> </script>
Adam,
Were you able to resolve this problem? I had the exact same issue with restoring my Front Page and can not get this resolved.
John
Hi
We had the same issue. I commented out the following lines within lib/weblib.php (around line number 2703) :
// if (!empty($CFG->messaging)) {
// $output .= message_popup_window();
// }
This results in no message popup window being displayed on log in or if the user browses the site even if you have a message waiting for you, but it is better than getting that unnecessary popup each time on log in and log out.
We have a message box on the site that shows if you have messages waiting for you, and users can still get an email with each new message.
Kaalgat.
We had the same issue. I commented out the following lines within lib/weblib.php (around line number 2703) :
// if (!empty($CFG->messaging)) {
// $output .= message_popup_window();
// }
This results in no message popup window being displayed on log in or if the user browses the site even if you have a message waiting for you, but it is better than getting that unnecessary popup each time on log in and log out.
We have a message box on the site that shows if you have messages waiting for you, and users can still get an email with each new message.
Kaalgat.
