After a recent upgrade to WordPress 3.5 on a multisite installation, I received an error when using “Update Network” through the GUI. I did some searching via WordPress forums and Google, but did not find anything specific to MU usage.
I did find a non-English site which offered a solution, but it required editing the files within WordPress, something which could be overwritten during an upgrade. The same page which offered the fix had a reference to another fix, which used an independent file which would eliminate the need to alter a standard system file. Below are both fixes, which I tested independently and verified as working with WordPress 3.5.
The original error was:
Warning! Problem updating https://sub.domain.tld. Your server may not be able to connect to sites running on it. Error message: SSL certificate problem, verify that the CA cert is OK. Details: error:14090086:SSL routines:SSL3_GET_SERVER_CERTIFICATE:certificate verify failed
The first fix, which is preferred, involved creating a directory and a php file.
Create the directory “mu-plugins” under /wp-content
Create a php file, using any name you want, and insert the following code.
Or you can edit the /wp-admin/network/upgrade.php file and the following code on line 68.
$response = wp_remote_get( $upgrade_url, array( 'timeout' => 120, 'httpversion' => '1.1', 'sslverify' => false ) );
After making the changes you can run the Update Network GUI and your sites will now upgrade.
This error was also referenced and answered here: http://wordpress.org/support/topic/failed-update-network-attempt-after-upgrading-to-341