Index: wp-includes/user.php
===================================================================
--- wp-includes/user.php	(revision 14190)
+++ wp-includes/user.php	(working copy)
@@ -258,6 +258,8 @@
  * global blog options. If the 'global' parameter is false, which it is by default
  * it will prepend the WordPress table prefix to the option name.
  *
+ * Deletes the user option if $newvalue is empty.
+ *
  * @since 2.0.0
  * @uses $wpdb WordPress database object for queries
  *
@@ -272,6 +274,12 @@
 
 	if ( !$global )
 		$option_name = $wpdb->prefix . $option_name;
+
+	// For backward compatibility.  See differences between update_user_meta() and deprecated update_user_meta().
+	// http://core.trac.wordpress.org/ticket/13088
+	if ( is_null( $newvalue ) || is_scalar( $newvalue ) && empty( $newvalue ) )
+		return delete_user_meta( $user_id, $option_name );
+
 	return update_user_meta( $user_id, $option_name, $newvalue );
 }
 
Index: wp-includes/ms-functions.php
===================================================================
--- wp-includes/ms-functions.php	(revision 14190)
+++ wp-includes/ms-functions.php	(working copy)
@@ -786,8 +786,8 @@
 		return false;
 
 	// Newly created users have no roles or caps until they are added to a blog.
-	update_user_option($user_id, 'capabilities', '');
-	update_user_option($user_id, 'user_level', '');
+	delete_user_option( $user_id, 'capabilities' );
+	delete_user_option( $user_id, 'user_level' );
 
 	do_action( 'wpmu_new_user', $user_id );