Index: wp-admin/includes/schema.php
===================================================================
--- wp-admin/includes/schema.php	(revision 20543)
+++ wp-admin/includes/schema.php	(working copy)
@@ -894,6 +894,7 @@
 		'illegal_names' => array( 'www', 'web', 'root', 'admin', 'main', 'invite', 'administrator', 'files' ),
 		'wpmu_upgrade_site' => $wp_db_version,
 		'welcome_email' => $welcome_email,
+		'welcome_user_email' => welcome_user_msg_filter(),
 		'first_post' => __( 'Welcome to <a href="SITE_URL">SITE_NAME</a>. This is your first post. Edit or delete it, then start blogging!' ),
 		// @todo - network admins should have a method of editing the network siteurl (used for cookie hash)
 		'siteurl' => get_option( 'siteurl' ) . '/',
Index: wp-admin/includes/upgrade.php
===================================================================
--- wp-admin/includes/upgrade.php	(revision 20543)
+++ wp-admin/includes/upgrade.php	(working copy)
@@ -1306,6 +1306,9 @@
 			update_site_option( 'allowedthemes', $converted );
 			delete_site_option( 'allowed_themes' );
 		}
+
+		if ( false === get_site_option( 'welcome_user_email' ) )
+			update_site_option( 'welcome_user_email', welcome_user_msg_filter() );
 	}
 }
 
Index: wp-includes/ms-functions.php
===================================================================
--- wp-includes/ms-functions.php	(revision 20543)
+++ wp-includes/ms-functions.php	(working copy)
@@ -1216,7 +1216,7 @@
 		return false;
 
 	$welcome_email = stripslashes( get_site_option( 'welcome_email' ) );
-	if ( $welcome_email == false )
+	if ( false == $welcome_email )
 		$welcome_email = stripslashes( __( 'Dear User,
 
 Your new SITE_NAME site has been successfully set up at:
@@ -1279,7 +1279,9 @@
 	if ( !apply_filters('wpmu_welcome_user_notification', $user_id, $password, $meta) )
 		return false;
 
-	$welcome_email = get_site_option( 'welcome_user_email' );
+	$welcome_email = stripslashes( get_site_option( 'welcome_user_email' ) );
+	if ( false == $welcome_email )
+		$welcome_email = welcome_user_msg_filter();
 
 	$user = new WP_User($user_id);
 
@@ -1885,14 +1887,14 @@
 add_filter('option_users_can_register', 'users_can_register_signup_filter');
 
 /**
- * Ensure that the welcome message is not empty. Currently unused.
+ * Ensure that the welcome message is not empty.
  *
  * @since MU
  *
  * @param string $text
  * @return string
  */
-function welcome_user_msg_filter( $text ) {
+function welcome_user_msg_filter( $text = false ) {
 	if ( !$text ) {
 		return __( 'Dear User,
 
@@ -1909,7 +1911,6 @@
 	}
 	return $text;
 }
-add_filter( 'site_option_welcome_user_email', 'welcome_user_msg_filter' );
 
 /**
  * Whether to force SSL on content.