Index: wp-admin/network/site-themes.php
===================================================================
--- wp-admin/network/site-themes.php	(revision 21272)
+++ wp-admin/network/site-themes.php	(working copy)
@@ -110,7 +110,7 @@
 			break;
 	}
 
-	update_option( 'allowedthemes', $allowed_themes );
+	update_blog_option( $id, 'allowedthemes', $allowed_themes );
 	restore_current_blog();
 
 	wp_safe_redirect( add_query_arg( array( 'id' => $id, $action => $n ), $referer ) );