I just upgraded a WordPress Network from 3.4.2 to 3.5.1. I went to Update Network (/wp-admin/network/upgrade.php), upon suggestion of the prompts. After hitting the Update Network button, I get this on the next page (/wp-admin/network/upgrade.php?action=upgrade):
Warning! Problem updating https://[hostname]/[nameOfFirstBlog]. Your server may not be able to connect to sites running on it. Error message: Peer certificate cannot be authenticated with known CA certificates
This is wrong. We are using a valid, non-expired certificate issued by InCommon Server CA, and it's issued to the correct URL for this server.
I have done network upgrades with this system before and have had no problem. It goes through all of my 100 or so blogs, one by one, and runs their respective upgrade scripts. It's not clear to me why this is happening with this upgrade? Is something wrong with 3.5.1's updater?