Ok, try disabling all your plug-ins because a hack maybe conflicting with the message box.
In your config.php after <?php add
define('DISABLE_HOOKS', true);
So the first two lines will look like this:
<?php
define('DISABLE_HOOKS', true);
Does it still happen? If so in AdminCP >> Maintenance >> Diagnostics >> Suspect File Versions then click Submit and see if vBulletin comes up with any file errors.
After you have tested all this, you can remove define('DISABLE_HOOKS', true); to turn all your hacks back on.
