Index: src/wp-includes/ms-settings.php
===================================================================
--- src/wp-includes/ms-settings.php	(revision 27404)
+++ src/wp-includes/ms-settings.php	(working copy)
@@ -113,8 +113,12 @@
 		ms_not_installed();
 	}
 
-	// @todo What if the domain of the network doesn't match the current site?
-	$current_site->cookie_domain = $current_site->domain;
+	// If the site domain differs from the network domain, defer to the site for cookies.
+	if ( isset( $current_blog->domain ) && $current_blog->domain !== $current_site->domain ) {
+		$current_site->cookie_domain = $current_blog->domain;
+	} else {
+		$current_site->cookie_domain = $current_site->domain;
+	}
 	if ( 'www.' === substr( $current_site->cookie_domain, 0, 4 ) ) {
 		$current_site->cookie_domain = substr( $current_site->cookie_domain, 4 );
 	}