diff --git a/wp-admin/includes/upgrade.php b/wp-admin/includes/upgrade.php
index 593e45b407..d8e8d7e6c9 100644
--- a/wp-admin/includes/upgrade.php
+++ b/wp-admin/includes/upgrade.php
@@ -1136,8 +1136,8 @@ function upgrade_300() {
 		$wpdb->update( $wpdb->postmeta, array( 'meta_value' => '' ), array( 'meta_key' => '_menu_item_target', 'meta_value' => '_self' ) );
 
 	// 3.0-beta metabox changes. can be removed before release. // r13551
-	if ( $wp_current_db_version >= 13309 && $wp_current_db_version < 14139 )
-		$wpdb->query( "DELETE FROM $wpdb->options WHERE option_name LIKE '%meta-box-hidden%' OR option_name LIKE '%closedpostboxes%'" );
+	if ( ( !is_multisite() || is_main_site() ) && $wp_current_db_version >= 13309 && $wp_current_db_version < 14139 )
+		$wpdb->query( "DELETE FROM $wpdb->usermeta WHERE meta_key LIKE '{$wpdb->base_prefix}%meta-box-hidden%' OR meta_key LIKE '{$wpdb->base_prefix}%closedpostboxes%'" );
 
 }