Had the same problem on one installation.
Reason was an incorrect setup inside wp-config.php:
define( 'DOMAIN_CURRENT_SITE', 'mydomain.com' );
define( 'SITE_ID_CURRENT_SITE', 1 );
define( 'BLOG_ID_CURRENT_SITE', 8 ); // << THIS WAS SET TO 1
As soon as I set the BLOG_ID_CURRENT_SITE to the right value of the “mydomain.com” blog it worked fine.
Hopefully this works for others as well and helps to fix this issue that did not happen before 3.1.